├── .gitignore ├── README.txt ├── autoace_config ├── INSTALL ├── brenneri.config ├── brenneri.merge.config ├── briggsae.config ├── briggsae.merge.config ├── brugia.config ├── brugia.merge.config ├── build_env.cshrc ├── check_file.config ├── elegans.config ├── genetic_code.ace ├── japonica.config ├── japonica.merge.config ├── misc_autoace_methods.ace ├── ovolvulus.config ├── ovolvulus.merge.config ├── pristionchus.config ├── pristionchus.merge.config ├── remanei.config ├── remanei.merge.config ├── sratti.config ├── sratti.merge.config ├── tmuris.config └── tmuris.merge.config ├── config ├── nematoda │ ├── Acanthocheilonema_viteae.ini │ ├── Ancylostoma_caninum.ini │ ├── Ancylostoma_ceylanicum.ini │ ├── Angiostrongylus_cantonensis.ini │ ├── Anguillicola_crassus.ini │ ├── Aphelenchoides_besseyi.ini │ ├── Aphelenchoides_fragariae.ini │ ├── Ascaris_suum.ini │ ├── Brugia_malayi.ini │ ├── Brugia_pahangi.ini │ ├── Bursaphelenchus_mucronatus.ini │ ├── Bursaphelenchus_xylophilus.ini │ ├── Caenorhabditis_afra.ini │ ├── Caenorhabditis_angaria.ini │ ├── Caenorhabditis_brenneri.ini │ ├── Caenorhabditis_briggsae.ini │ ├── Caenorhabditis_castelli.ini │ ├── Caenorhabditis_doughertyi.ini │ ├── Caenorhabditis_elegans.ini │ ├── Caenorhabditis_guadeloupensis.ini │ ├── Caenorhabditis_japonica.ini │ ├── Caenorhabditis_macrosperma.ini │ ├── Caenorhabditis_nouraguensis.ini │ ├── Caenorhabditis_plicata.ini │ ├── Caenorhabditis_remanei.ini │ ├── Caenorhabditis_sp._10_JR-2014.ini │ ├── Caenorhabditis_sp._1_KK-2011.ini │ ├── Caenorhabditis_sp._21_LS-2015.ini │ ├── Caenorhabditis_sp._26_LS-2015.ini │ ├── Caenorhabditis_sp._31_LS-2015.ini │ ├── Caenorhabditis_sp._32_LS-2015.ini │ ├── Caenorhabditis_sp._38_MB-2015.ini │ ├── Caenorhabditis_sp._39_LS-2015.ini │ ├── Caenorhabditis_sp._40_LS-2015.ini │ ├── Caenorhabditis_sp._43_LS-2015.ini │ ├── Caenorhabditis_virilis.ini │ ├── Caenorhabditis_wallacei.ini │ ├── Cooperia_oncophora.ini │ ├── Cylicostephanus_goldi.ini │ ├── Deladenus_siricidicola.ini │ ├── Dictyocaulus_filaria.ini │ ├── Dictyocaulus_viviparus.ini │ ├── Dirofilaria_immitis.ini │ ├── Enoplus_brevis.ini │ ├── Globodera_pallida.ini │ ├── Globodera_rostochiensis.ini │ ├── Haemonchus_contortus.ini │ ├── Halomonhystera_disjuncta.ini │ ├── Halomonhystera_hermesi.ini │ ├── Heligmosomoides_polygyrus.ini │ ├── Heterodera_avenae.ini │ ├── Heterodera_glycines.ini │ ├── Heterodera_schachtii.ini │ ├── Heterorhabditis_indica.ini │ ├── Hirschmanniella_oryzae.ini │ ├── Litomosoides_sigmodontis.ini │ ├── Loa_loa.ini │ ├── Longidorus_elongatus.ini │ ├── Mecistocirrus_digitatus.ini │ ├── Meloidogyne_graminicola.ini │ ├── Meloidogyne_incognita.ini │ ├── Nacobbus_aberrans.ini │ ├── Necator_americanus.ini │ ├── Oesophagostomum_dentatum.ini │ ├── Onchocerca_ochengi.ini │ ├── Onchocerca_volvulus.ini │ ├── Ostertagia_ostertagi.ini │ ├── Panagrellus_redivivus.ini │ ├── Panagrolaimus_davidi.ini │ ├── Pratylenchus_coffeae.ini │ ├── Pratylenchus_penetrans.ini │ ├── Pratylenchus_zeae.ini │ ├── Prionchulus_punctatus.ini │ ├── Pristionchus_pacificus.ini │ ├── Rotylenchulus_reniformis.ini │ ├── Setaria_labiatopapillosa.ini │ ├── Steinernema_carpocapsae.ini │ ├── Steinernema_feltiae.ini │ ├── Strongyloides_ratti.ini │ ├── Strongyloides_stercoralis.ini │ ├── Strongyloides_venezuelensis.ini │ ├── Teladorsagia_circumcincta.ini │ ├── Toxocara_canis.ini │ ├── Trichinella_britovi.ini │ ├── Trichinella_murrelli.ini │ ├── Trichinella_nativa.ini │ ├── Trichinella_nelsoni.ini │ ├── Trichinella_papuae.ini │ ├── Trichinella_patagoniensis.ini │ ├── Trichinella_pseudospiralis.ini │ ├── Trichinella_sp._T6.ini │ ├── Trichinella_sp._T8.ini │ ├── Trichinella_sp._T9.ini │ ├── Trichinella_spiralis.ini │ ├── Trichinella_zimbabwensis.ini │ ├── Trichostrongylus_colubriformis.ini │ ├── Trichuris_muris.ini │ ├── Trichuris_suis.ini │ └── Trichuris_trichiura.ini ├── platyhelminthes │ ├── Bdellocephala_annandalei.ini │ ├── Bdelloura_candida.ini │ ├── Bothriomolus_balticus.ini │ ├── Bothrioplana_semperi.ini │ ├── Catenula_lemnae.ini │ ├── Clonorchis_sinensis.ini │ ├── Dendrocoelum_lacteum.ini │ ├── Dugesia_japonica.ini │ ├── Echinococcus.ini │ ├── Echinococcus_granulosus.ini │ ├── Echinococcus_multilocularis.ini │ ├── Echinoplana_celerrima.ini │ ├── Fasciola_gigantica.ini │ ├── Fasciola_hepatica.ini │ ├── Fascioloides_magna.ini │ ├── Fasciolopsis_buski.ini │ ├── Geocentrophora_applanata.ini │ ├── Geocentrophora_sphyrocephala.ini │ ├── Girardia.ini │ ├── Girardia_dorotocephala.ini │ ├── Girardia_tigrina.ini │ ├── Gnosonesimida_sp._IV_CEL-2015.ini │ ├── Hymenolepis_microstoma.ini │ ├── Itaspiella_helgolandica.ini │ ├── Kronborgia_cf._amphipodicola_CEL-2015.ini │ ├── Lehardyia_sp._CEL-2015.ini │ ├── Leptoplana_tremellaris.ini │ ├── Macrostomum_cf._ruebushi_CEL-2015.ini │ ├── Macrostomum_lignano.ini │ ├── Maritigrella_crozieri.ini │ ├── Mesostoma_lingua.ini │ ├── Microdalyellia_fusca.ini │ ├── Microdalyellia_schmidti.ini │ ├── Microdalyellia_sp._CEL-2015.ini │ ├── Microstomum_lineare.ini │ ├── Monocelis_fusca.ini │ ├── Monocelis_sp._BE-2015.ini │ ├── Nematoplana_coelogynoporoides.ini │ ├── Opisthorchis_felineus.ini │ ├── Opisthorchis_viverrini.ini │ ├── Paragonimus_kellicotti.ini │ ├── Paragonimus_miyazakii.ini │ ├── Paragonimus_skrjabini.ini │ ├── Paragonimus_westermani.ini │ ├── Paramphistomum_cervi.ini │ ├── Phagocata_gracilis.ini │ ├── Phagocata_morgani.ini │ ├── Procotyla_fluviatilis.ini │ ├── Prorhynchus_alpinus.ini │ ├── Prorhynchus_sp._I_CEL-2015.ini │ ├── Prorhynchus_stagnalis.ini │ ├── Prosogynopora_riseri.ini │ ├── Prostheceraeus_vittatus.ini │ ├── Prosthiostomum_siphunculus.ini │ ├── Protomonotresidae_sp._CEL-2015.ini │ ├── Provortex_cf._sphagnorum_CEL-2015.ini │ ├── Rhynchomesostoma_rostratum.ini │ ├── Schistocephalus_solidus.ini │ ├── Schistosoma_japonicum.ini │ ├── Schistosoma_mansoni.ini │ ├── Schistosoma_turkestanicum.ini │ ├── Schmidtea_mediterranea.ini │ ├── Schmidtea_polychroa.ini │ ├── Solenopharyngidae_sp._CEL-2015.ini │ ├── Stenostomum_leucops.ini │ ├── Stenostomum_sthenum.ini │ ├── Stylochoplana_maculata.ini │ ├── Stylochus_ellipticus.ini │ ├── Taenia_asiatica.ini │ ├── Taenia_crassiceps.ini │ ├── Taenia_multiceps.ini │ ├── Taenia_pisiformis.ini │ ├── Taenia_saginata.ini │ └── Xenoprorhynchus_sp._I_CEL-2015.ini └── worm │ ├── Acanthocheilonema_viteae.ini │ ├── Ancylostoma_caninum.ini │ ├── Ancylostoma_ceylanicum.ini │ ├── Angiostrongylus_cantonensis.ini │ ├── Anguillicola_crassus.ini │ ├── Aphelenchoides_besseyi.ini │ ├── Aphelenchoides_fragariae.ini │ ├── Ascaris_suum.ini │ ├── Bdellocephala_annandalei.ini │ ├── Bdelloura_candida.ini │ ├── Bothriomolus_balticus.ini │ ├── Bothrioplana_semperi.ini │ ├── Brugia_malayi.ini │ ├── Brugia_pahangi.ini │ ├── Bursaphelenchus_mucronatus.ini │ ├── Bursaphelenchus_xylophilus.ini │ ├── Caenorhabditis_afra.ini │ ├── Caenorhabditis_angaria.ini │ ├── Caenorhabditis_brenneri.ini │ ├── Caenorhabditis_briggsae.ini │ ├── Caenorhabditis_castelli.ini │ ├── Caenorhabditis_doughertyi.ini │ ├── Caenorhabditis_elegans.ini │ ├── Caenorhabditis_guadeloupensis.ini │ ├── Caenorhabditis_japonica.ini │ ├── Caenorhabditis_macrosperma.ini │ ├── Caenorhabditis_nouraguensis.ini │ ├── Caenorhabditis_plicata.ini │ ├── Caenorhabditis_remanei.ini │ ├── Caenorhabditis_sp._10_JR-2014.ini │ ├── Caenorhabditis_sp._1_KK-2011.ini │ ├── Caenorhabditis_sp._21_LS-2015.ini │ ├── Caenorhabditis_sp._26_LS-2015.ini │ ├── Caenorhabditis_sp._31_LS-2015.ini │ ├── Caenorhabditis_sp._32_LS-2015.ini │ ├── Caenorhabditis_sp._38_MB-2015.ini │ ├── Caenorhabditis_sp._39_LS-2015.ini │ ├── Caenorhabditis_sp._40_LS-2015.ini │ ├── Caenorhabditis_sp._43_LS-2015.ini │ ├── Caenorhabditis_virilis.ini │ ├── Caenorhabditis_wallacei.ini │ ├── Catenula_lemnae.ini │ ├── Clonorchis_sinensis.ini │ ├── Cooperia_oncophora.ini │ ├── Cylicostephanus_goldi.ini │ ├── Deladenus_siricidicola.ini │ ├── Dendrocoelum_lacteum.ini │ ├── Dictyocaulus_filaria.ini │ ├── Dictyocaulus_viviparus.ini │ ├── Dirofilaria_immitis.ini │ ├── Dugesia_japonica.ini │ ├── Echinococcus_granulosus.ini │ ├── Echinococcus_multilocularis.ini │ ├── Echinoplana_celerrima.ini │ ├── Enoplus_brevis.ini │ ├── Fasciola_gigantica.ini │ ├── Fasciola_hepatica.ini │ ├── Fascioloides_magna.ini │ ├── Fasciolopsis_buski.ini │ ├── Geocentrophora_applanata.ini │ ├── Geocentrophora_sphyrocephala.ini │ ├── Girardia.ini │ ├── Girardia_dorotocephala.ini │ ├── Girardia_tigrina.ini │ ├── Globodera_pallida.ini │ ├── Globodera_rostochiensis.ini │ ├── Gnosonesimida_sp._IV_CEL-2015.ini │ ├── Haemonchus_contortus.ini │ ├── Halomonhystera_disjuncta.ini │ ├── Halomonhystera_hermesi.ini │ ├── Heligmosomoides_polygyrus.ini │ ├── Heterodera_avenae.ini │ ├── Heterodera_glycines.ini │ ├── Heterodera_schachtii.ini │ ├── Heterorhabditis_indica.ini │ ├── Hirschmanniella_oryzae.ini │ ├── Hymenolepis_microstoma.ini │ ├── Itaspiella_helgolandica.ini │ ├── Kronborgia_cf._amphipodicola_CEL-2015.ini │ ├── Lehardyia_sp._CEL-2015.ini │ ├── Leptoplana_tremellaris.ini │ ├── Litomosoides_sigmodontis.ini │ ├── Loa_loa.ini │ ├── Longidorus_elongatus.ini │ ├── Macrostomum_cf._ruebushi_CEL-2015.ini │ ├── Macrostomum_lignano.ini │ ├── Maritigrella_crozieri.ini │ ├── Mecistocirrus_digitatus.ini │ ├── Meloidogyne_graminicola.ini │ ├── Meloidogyne_incognita.ini │ ├── Mesostoma_lingua.ini │ ├── Microdalyellia_fusca.ini │ ├── Microdalyellia_schmidti.ini │ ├── Microdalyellia_sp._CEL-2015.ini │ ├── Microstomum_lineare.ini │ ├── Monocelis_fusca.ini │ ├── Monocelis_sp._BE-2015.ini │ ├── Nacobbus_aberrans.ini │ ├── Necator_americanus.ini │ ├── Nematoplana_coelogynoporoides.ini │ ├── Oesophagostomum_dentatum.ini │ ├── Onchocerca_ochengi.ini │ ├── Onchocerca_volvulus.ini │ ├── Opisthorchis_felineus.ini │ ├── Opisthorchis_viverrini.ini │ ├── Ostertagia_ostertagi.ini │ ├── Panagrellus_redivivus.ini │ ├── Panagrolaimus_davidi.ini │ ├── Paragonimus_kellicotti.ini │ ├── Paragonimus_miyazakii.ini │ ├── Paragonimus_skrjabini.ini │ ├── Paragonimus_westermani.ini │ ├── Paramphistomum_cervi.ini │ ├── Phagocata_gracilis.ini │ ├── Pratylenchus_coffeae.ini │ ├── Pratylenchus_penetrans.ini │ ├── Pratylenchus_zeae.ini │ ├── Prionchulus_punctatus.ini │ ├── Pristionchus_pacificus.ini │ ├── Procotyla_fluviatilis.ini │ ├── Prorhynchus_alpinus.ini │ ├── Prorhynchus_sp._I_CEL-2015.ini │ ├── Prorhynchus_stagnalis.ini │ ├── Prosogynopora_riseri.ini │ ├── Prostheceraeus_vittatus.ini │ ├── Prosthiostomum_siphunculus.ini │ ├── Protomonotresidae_sp._CEL-2015.ini │ ├── Provortex_cf._sphagnorum_CEL-2015.ini │ ├── Rhynchomesostoma_rostratum.ini │ ├── Rotylenchulus_reniformis.ini │ ├── Schistocephalus_solidus.ini │ ├── Schistosoma_japonicum.ini │ ├── Schistosoma_mansoni.ini │ ├── Schmidtea_mediterranea.ini │ ├── Schmidtea_polychroa.ini │ ├── Setaria_labiatopapillosa.ini │ ├── Solenopharyngidae_sp._CEL-2015.ini │ ├── Steinernema_carpocapsae.ini │ ├── Steinernema_feltiae.ini │ ├── Stenostomum_leucops.ini │ ├── Stenostomum_sthenum.ini │ ├── Strongyloides_ratti.ini │ ├── Strongyloides_stercoralis.ini │ ├── Strongyloides_venezuelensis.ini │ ├── Stylochoplana_maculata.ini │ ├── Stylochus_ellipticus.ini │ ├── Taenia_crassiceps.ini │ ├── Taenia_multiceps.ini │ ├── Taenia_pisiformis.ini │ ├── Taenia_saginata.ini │ ├── Teladorsagia_circumcincta.ini │ ├── Toxocara_canis.ini │ ├── Trichinella_britovi.ini │ ├── Trichinella_murrelli.ini │ ├── Trichinella_nativa.ini │ ├── Trichinella_nelsoni.ini │ ├── Trichinella_papuae.ini │ ├── Trichinella_patagoniensis.ini │ ├── Trichinella_pseudospiralis.ini │ ├── Trichinella_sp._T6.ini │ ├── Trichinella_sp._T8.ini │ ├── Trichinella_sp._T9.ini │ ├── Trichinella_spiralis.ini │ ├── Trichinella_zimbabwensis.ini │ ├── Trichostrongylus_colubriformis.ini │ ├── Trichuris_muris.ini │ ├── Trichuris_suis.ini │ ├── Trichuris_trichiura.ini │ └── Xenoprorhynchus_sp._I_CEL-2015.ini ├── cpanfile ├── for_cvs ├── Blat.pm ├── RNAi_mapping_Igor │ ├── RunBlat.pl │ ├── igor.readme │ └── rnai_curation ├── agp2fasta.pl ├── crc64fasta.pl ├── ens_genome_xrefs.pl ├── genbank2gff.pl ├── getConservationScores.pl ├── gff_db_schema.sql ├── ortho2ace.rb ├── ortho_mcl.rb ├── process_ensembl_2_omim_data.pl ├── show_mult_align ├── show_mult_align2 └── update_hs_protein_list.pl ├── parasite ├── checks │ ├── Blast.dump.pl │ ├── FTP.dump.pl │ ├── biomart_taxon_tree.t │ ├── did_pipelines_run.t │ ├── ftp.t │ ├── golden_species_regex.t │ ├── jbrowse.t │ └── rest.t ├── modules │ ├── AFDB_import │ │ ├── HiveLoadAlphaFoldDBProteinFeatures.pm │ │ └── MakeAlphaFoldDBProteinFeatures.pm │ ├── CoreCreation │ │ ├── Conf.pm │ │ ├── Config │ │ │ └── Utils.pm │ │ ├── Fasta.pm │ │ ├── GFF3 │ │ │ └── Utils.pm │ │ └── gfftools.py │ ├── DumpCoreDatabases │ │ ├── BlastDumper.pm │ │ └── FtpDumper.pm │ ├── GenomeBrowser │ │ ├── Deployment.pm │ │ ├── JBrowseDisplay.pm │ │ ├── JBrowseDisplay │ │ │ ├── AnnotationTracks.pm │ │ │ ├── RnaseqTracks.pm │ │ │ └── SequenceTrack.pm │ │ ├── JBrowseTools.pm │ │ └── RnaseqHub.pm │ ├── IdMapping │ │ ├── TemporaryIdGenerator.pm │ │ └── history2events.py │ ├── MysqlPair.pm │ ├── Phenotypes.pm │ ├── PipeConfig │ │ ├── DumpCoreDatabases_conf.pm │ │ ├── ParaSiteLoadMembers_conf.pm │ │ └── ParaSiteRepeatModeler2_conf.pm │ ├── ProductionMysql.pm │ ├── SpeciesFtp.pm │ ├── XrefMapper │ │ ├── genedb.pm │ │ ├── parasite.pm │ │ └── wormbase.pm │ └── python │ │ ├── Deployment.py │ │ ├── GenomeBrowser │ │ ├── deploy_hub_data_to_embassy.py │ │ ├── deploy_web_data_to_embassy.py │ │ └── deploy_web_data_to_ftp.py │ │ ├── LSF.py │ │ ├── ProductionMysql.py │ │ ├── ProductionUtils.py │ │ ├── bash_commands.py │ │ └── handlers.py ├── scripts │ └── production │ │ ├── .add_orthologs_to_ftp.pl.swp │ │ ├── .compare_ftp_dirs.pl.swp │ │ ├── add_orthologs_to_ftp.pl │ │ ├── additional_jbrowse_tracks.sh │ │ ├── apollo │ │ ├── add_rnaseq.py │ │ ├── add_wbps_jbrowse_rnaseq_tracks_to_apollo.py │ │ ├── add_wbps_jbrowse_rnaseq_tracks_to_apollo_codon.py │ │ ├── create_new_apollo_instance.py │ │ ├── dependencies.py │ │ ├── fastq2counts.py │ │ ├── find_rnaseq_studies.py │ │ ├── sanger_prepare.sh │ │ ├── spawn_instance.sh │ │ └── tools.py │ │ ├── archive │ │ ├── archive.sh │ │ ├── mapping_conf.pl │ │ └── upload_mapping_as_history.pl │ │ ├── atacseq │ │ ├── Snakeatac │ │ └── config.yml │ │ ├── compara │ │ ├── parasite_hal_debug.pl │ │ ├── parasite_update_compara_master.pl │ │ ├── parasite_update_compara_master_for_hal.pl │ │ └── prepare_species_list.pl │ │ ├── compare_ftp_dirs.pl │ │ ├── compare_local_ftp_with_ftp_checksum.sh │ │ ├── copy-and-patch.sh │ │ ├── copy-db-to-rel.sh │ │ ├── copy_to_gxa_staging_area.pl │ │ ├── core-creation │ │ ├── assembly2jira.py │ │ ├── busco_parse_and_update.py │ │ ├── change_transcripts_to_noncoding.pl │ │ ├── change_transcripts_to_nontranslating_CDS.pl │ │ ├── create_otherfeatures_db.sh │ │ ├── dump_translations.pl │ │ ├── fasta_parsing_commands.sh │ │ ├── geneCounter.py │ │ ├── generate_analysis_desc_templates.py │ │ ├── gff_parsing_commands.sh │ │ ├── gff_utils.py │ │ ├── healthcheck.pl │ │ ├── healthcheck.sh │ │ ├── load_synonyms.pl │ │ ├── populate_analysis_descriptions_from_file.pl │ │ ├── populate_analysis_descriptions_in_cores_from_prod_db.pl │ │ ├── prepare_conf_and_fasta.pl │ │ ├── reformat_gff.py │ │ ├── reformat_gff_dependencies.py │ │ ├── reformat_gff_old.py │ │ ├── remove_scaffolds_from_fasta.py │ │ ├── set_karyotype_ranks.pl │ │ ├── update_logicnames.pl │ │ ├── update_taxonomy.py │ │ └── wb_descriptions │ │ │ ├── main.py │ │ │ ├── parsers.py │ │ │ └── utils.py │ │ ├── create_config_file_for_datachecks.sh │ │ ├── create_ensembl_metadata_db.sh │ │ ├── create_wormbase_conf.pl │ │ ├── datachecks │ │ ├── extract_nontranslating_transcripts.py │ │ ├── summarise_geneset_datacheck.py │ │ └── update_nontranslating_transcripts_in_db.py │ │ ├── dump_biomart_for_gprofiler.sh │ │ ├── dump_repeats.py │ │ ├── ensembl_handover │ │ ├── copy_and_patch_handover.sh │ │ ├── create_config_file_for_handover_datachecks.sh │ │ ├── create_ensembl_metadata_db_handover.sh │ │ ├── create_registry_for_handover.sh │ │ └── fix_handover_dbs.sh │ │ ├── fixes_patches │ │ ├── staging_patch_pull492 │ │ │ ├── copy_descriptions.sh │ │ │ ├── fix_display_xrefs.pl │ │ │ └── staging_patch_pull492.sh │ │ ├── staging_patch_pull526 │ │ │ ├── ascaris_suum_core_54_107_1.sql │ │ │ ├── copy_descriptions.sh │ │ │ ├── db_correspondance.tsv │ │ │ ├── hymenolepis_microstoma_core_54_107_1.sql │ │ │ ├── necator_americanus_core_54_107_1.sql │ │ │ ├── schistosoma_mansoni_core_54_107_1.sql │ │ │ └── staging_patch_pull526.sh │ │ ├── wbps17_biomart_AFDBproteinfeatures_patch │ │ │ └── patch.sh │ │ ├── wbps17_compara_CheckSpeciesSetSizeByMethod_patch │ │ │ └── patch.sql │ │ ├── wbps18_xrefs_XrefRunCriticalDatacheck_patch │ │ │ ├── Snakerestore │ │ │ ├── Snakexref │ │ │ ├── config.yml │ │ │ └── correct_nontranslating_cds.py │ │ └── wbps_ftp_dumps │ │ │ └── wbps_ftp_dump_genome_fix.sh │ │ ├── genebuild.sh │ │ ├── get_bioproject.py │ │ ├── get_ftp_bioproject.py │ │ ├── id_minting │ │ └── create_db.sql │ │ ├── inflate_conf.pl │ │ ├── jbrowse_tracks_and_hub.pl │ │ ├── make_parasite_FTP_site.pl │ │ ├── ncbi │ │ ├── assemblies_for_taxon.pl │ │ ├── calculate_fasta_sequences_lengths.pl │ │ ├── check_ncbi.sh │ │ ├── check_ncbi_filter.pl │ │ ├── check_ncbi_quick.sh │ │ ├── compare_docs_against_current_staging.pl │ │ ├── doc_for_assembly.pl │ │ └── prepare_data_folder.pl │ │ ├── new_release_setup │ │ ├── checkout_git_repos.sh │ │ ├── checkout_git_repos_brc4rnaseq.sh │ │ ├── checkout_git_repos_genebuild.sh │ │ ├── fix_dbs_as_per_ensembl_dbs.sh │ │ └── retrieve_comparators.sh │ │ ├── nextflow │ │ ├── modules │ │ │ ├── README.md │ │ │ ├── busco │ │ │ │ ├── busco_augustus_species.nf │ │ │ │ ├── busco_dataset.nf │ │ │ │ ├── busco_genome_factory.nf │ │ │ │ ├── busco_genome_run.nf │ │ │ │ ├── busco_protein_run.nf │ │ │ │ ├── fetch_genome.nf │ │ │ │ ├── fetch_proteins.nf │ │ │ │ └── species_outdir.nf │ │ │ ├── database │ │ │ │ ├── db_factory.nf │ │ │ │ └── dump_db.nf │ │ │ ├── omark │ │ │ │ ├── omamer_hog.nf │ │ │ │ └── run_omark.nf │ │ │ └── utils │ │ │ │ ├── parse_output.nf │ │ │ │ └── utils.nf │ │ ├── subworkflows │ │ │ ├── README.md │ │ │ └── busco_dataset │ │ │ │ └── main.nf │ │ └── workflows │ │ │ ├── busco_pipeline │ │ │ ├── busco.nf │ │ │ └── nextflow.config │ │ │ └── nextflow.config │ │ ├── reciprocal_best_blast_hit.sh │ │ ├── release_summary.pl │ │ ├── remove_dups.pl │ │ ├── rename_wb_species.sh │ │ ├── rnaseq │ │ ├── Alignments │ │ │ └── bash_commands.py │ │ ├── Reads │ │ │ └── bash_commands.py │ │ ├── Utils.py │ │ ├── __init__.py │ │ ├── brc4 │ │ │ ├── brc4_create_input_from_pre-run_status_json.py │ │ │ ├── brc4_create_tpm_for_existing_counts.sh │ │ │ ├── brc4_create_tpm_for_existing_counts_wrapper.sh │ │ │ ├── brc4_make_dir_for_gene_exp.py │ │ │ ├── brc4_release_update_for_pipeline.py │ │ │ ├── compare_with_rnaseqer.sh │ │ │ ├── compare_with_rnaseqer_tpm.sh │ │ │ ├── comparison_plots.R │ │ │ ├── comparison_plots_tpm.R │ │ │ ├── create_registry_for_brc4.sh │ │ │ └── deploy-replace_new_bigwigs.py │ │ ├── dependencies.py │ │ ├── fastq2counts.py │ │ ├── get_ena_isoseq_studies_by_taxon_id.py │ │ ├── get_ena_studies_by_taxon_id.py │ │ ├── get_ena_studies_by_taxon_id_per_year.py │ │ ├── get_ena_studies_scRNASeq_by_taxon_id.py │ │ ├── intron_for_apollo_bams.py │ │ ├── jbrowse_smansoni.py │ │ └── tools.py │ │ ├── run_ensembl_healthcheck.sh │ │ ├── set_core_samples.pl │ │ ├── set_web_data_to_default.pl │ │ ├── setup_PARASITE_CONF_folder.pl │ │ ├── stringdb │ │ ├── common_species.py │ │ ├── genes.py │ │ ├── parsers.py │ │ ├── proteins.py │ │ ├── utils.py │ │ └── wbps_stringdb_organisms.py.bak │ │ ├── summarise_geneset_datacheck.py │ │ ├── sync_metakeys_between_core_prod.py │ │ ├── update_isl_genomes.pl │ │ ├── variation │ │ ├── add_external_db_name.py │ │ ├── create_variation_registry_for_species.sh │ │ ├── dump_homology_phenotypes.py │ │ ├── dump_phenotypes.pl │ │ ├── gaf_file_validator.py │ │ ├── id_to_external_db_name.py │ │ ├── parse_ipcress.pl │ │ ├── parse_wbrnaidump.py │ │ ├── wb_celegans_phenotypes │ │ │ ├── cele_pheno_datacheck.py │ │ │ ├── dump_homology_phenotypes.py │ │ │ ├── helpers.py │ │ │ └── import_celegans_wormbase.py │ │ └── wbrnaitools.py │ │ ├── whole_genome_alignments │ │ ├── GenomicAlignBlock_example.pl │ │ ├── add_hal_file_to_master.sh │ │ ├── busco_n50_for_release.py │ │ ├── create_cactus_hal_pw_mlsses.pl │ │ ├── create_cactus_seqfile.py │ │ ├── download_psftp_fasta.sh │ │ ├── dump_hal_genome_ids.pl │ │ └── slurm.yaml │ │ └── xref │ │ ├── afdb_name_check.sh │ │ ├── afdb_wbps_generate_mapping_files.pl │ │ ├── afdb_wbps_load_features.sh │ │ ├── gaf_to_gpad.pl │ │ ├── ini_to_json.pl │ │ ├── ini_to_species.pl │ │ ├── our_ini.pl │ │ ├── prepare_for_xrefs.sh │ │ ├── prepare_gpad_files.sh │ │ ├── repair_xref_tables.sh │ │ ├── separate_gpad_by_species.pl │ │ ├── wormbase_datacheck.sh │ │ └── xref_diff_tools.sh └── t │ └── GenomeBrowser │ └── JBrowseDisplay.t ├── scripts ├── AGR │ ├── agr_orthologs.pl │ ├── agr_variations.def │ ├── agr_variations_json2vcf.py │ ├── curation_db_submissions │ │ ├── make_agr_agm_component_associations_json.pl │ │ ├── make_agr_agm_json.pl │ │ ├── make_agr_allele_json.pl │ │ ├── make_agr_construct_json.pl │ │ ├── make_agr_disease_json.pl │ │ └── make_agr_gene_json.pl │ ├── data_submission.pl │ ├── get_chebi_name_map.pl │ ├── import_AGR_OMIM_xrefs.pl │ ├── import_AGR_gene_objects.pl │ ├── make_agr_AGM.pl │ ├── make_agr_DAF.pl │ ├── make_agr_HTS.pl │ ├── make_agr_allele_json.pl │ ├── make_agr_basic_gene_json.pl │ ├── make_agr_construct_json.pl │ ├── make_agr_disease_json.pl │ ├── make_agr_expression_json.pl │ ├── make_agr_genetic_interaction_psimitab.pl │ ├── make_agr_gff.pl │ ├── make_agr_interactions_psimitab.pl │ ├── make_agr_molecules.pl │ ├── make_agr_phenotype_json.pl │ ├── make_agr_reference_json.pl │ ├── make_agr_variations.rb │ └── run_agr_vep_pipelines.pl ├── BLAST_scripts │ ├── ABC.pl │ ├── GSI.pm │ ├── acc2clone.txt │ ├── blast_builder.pl │ ├── blast_kill_list.pl │ ├── blastfilter.pl │ ├── blastx_dump.pl │ ├── convert_chromblast2clone.pl │ ├── copy_files_to_acari.pl │ ├── dump.pl │ ├── dump_TRF.pl │ ├── dump_blastp_from_file.pl │ ├── dump_blastx.pl │ ├── dump_interpro_motif.pl │ ├── dump_motif.pl │ ├── dump_one_new.pl │ ├── dump_protein_features.pl │ ├── dump_repeats.pl │ ├── ensembl_blat.pl │ ├── ensembl_genblast.pl │ ├── fasta2agp.pl │ ├── fasta2gsi.pl │ ├── find_duplicate_clones.pl │ ├── gff2cds.pl │ ├── gff2cos.pl │ ├── human_peps2dmp.pl │ ├── inverted.pl │ ├── make_flypepfile.pl │ ├── make_humanpepfile.pl │ ├── make_interpro.pl │ ├── make_yeastpepfile.pl │ ├── map_gff.pl │ ├── map_gff_fails.pl │ ├── parse_IPI_human.pl │ ├── pmatch.pl │ ├── supercontig_split.pl │ ├── swiss_trembl2dbm.pl │ ├── swiss_trembl2slim.pl │ ├── update_SWALL.pl │ ├── update_blastDBs.pl │ ├── write.swiss_trembl.pl │ └── write_ipi_info.pl ├── BLAT2GFF.pl ├── BLAT_controller.pl ├── BuildLocks.pm ├── CDS.pl ├── CRC64.pm ├── Coords_converter.pm ├── Dump_Subseq.pl ├── Dump_new_prot_only.pl ├── EMBL_Sequencefetch.pl ├── EMBLdump.pl ├── EMBLsubmit.pl ├── EMBLupdate.pl ├── ENSEMBL │ ├── analysis.descriptions │ ├── attrib_type.sql │ ├── doc │ │ ├── converting_wormbase_to_ensembl.txt │ │ └── howto │ ├── etc │ │ ├── E_registry.pl │ │ ├── efg.config │ │ ├── ensembl_environment.csh │ │ ├── ensembl_lite.conf.example │ │ ├── est_star_setup.csh │ │ ├── interproscan_setup.sh │ │ └── njtree.12.worm_compara_test_orthotree.nh │ ├── lib │ │ ├── Clone2Acc.pm │ │ ├── Domain2Interpro.pm │ │ ├── WormBase2Ensembl.pm │ │ ├── WormFeature.pm │ │ ├── WormFeature │ │ │ ├── Blat.pm │ │ │ └── WublastX.pm │ │ └── Wormy.pm │ ├── scripts │ │ ├── add_new_species_web_data_to_prod_db.pl │ │ ├── add_seq_region_synonyms.pl │ │ ├── affy.rb │ │ ├── agilent.rb │ │ ├── analysis_setup.pl │ │ ├── assign_external_db_ids.pl │ │ ├── blastx_store.pl │ │ ├── check_genes.pl │ │ ├── count_scaffolds.pl │ │ ├── delete_genes.pl │ │ ├── dump_all_clustal.pl │ │ ├── dump_clustal.pl │ │ ├── dump_genome.pl │ │ ├── dump_gff3.pl │ │ ├── dump_gtf_from_ensembl.pl │ │ ├── dump_gtf_from_gff3.pl │ │ ├── dump_oligo_sets_from_ensembl.pl │ │ ├── dump_pairwise.pl │ │ ├── dump_proteins.pl │ │ ├── dump_transcripts.pl │ │ ├── ensembl2gtf_lite.pl │ │ ├── est_star_hive.pl │ │ ├── expr_store.pl │ │ ├── feature_store.pl │ │ ├── genbank2gff3.pl │ │ ├── gene_stats.pl │ │ ├── gene_store.pl │ │ ├── getConservationScores.pl │ │ ├── get_all_elegans_orthologues.pl │ │ ├── get_cgc_orthologs.pl │ │ ├── get_max_intron_size.pl │ │ ├── get_non_core_species_EST.pl │ │ ├── get_omim2ensemblprotein.pl │ │ ├── get_one2oneTrees.pl │ │ ├── getsynteny.pl │ │ ├── gff32ensembl_simple.pl │ │ ├── kill_transcripts.pl │ │ ├── load_analysis_descriptions.pl │ │ ├── operon_store.pl │ │ ├── parse_log.pl │ │ ├── prepare_modelorganism_data.pl │ │ ├── process_t3_gff.pl │ │ ├── pseudo_store.pl │ │ ├── raw_compute_transfer.pl │ │ ├── rename_gene-transcript_stable_ids.sh │ │ ├── rnai_store.pl │ │ ├── sequence_store.pl │ │ ├── set_codon_table.pl │ │ ├── sl1_store.pl │ │ ├── sl2_store.pl │ │ ├── split_genome_for_ensembl.pl │ │ ├── split_wig.pl │ │ ├── transfer_ensembl_features.pl │ │ ├── translation_check.pl │ │ ├── update_compara_master.pl │ │ ├── update_ensembl_orthologs.pl │ │ ├── update_ipi_accession.pl │ │ ├── update_nontranslating_transcripts_in_db.py │ │ ├── worm_lite.pl │ │ ├── worm_lite_wormbase.pl │ │ ├── wormbase_gene_xrefs.pl │ │ └── wormbase_to_ensembl.pl │ └── tests │ │ ├── compara_tests.pl │ │ ├── test.gff │ │ ├── test.yml │ │ └── wormy.t ├── Feature_mapper.pm ├── GENEACE │ ├── EMBL_feature_parser.pm │ ├── Geneace.pm │ ├── NStest.pl │ ├── Update_Biotype.pl │ ├── batch_addname.pl │ ├── batch_delName.pl │ ├── batch_features.pl │ ├── batch_genes.pl │ ├── batch_kill.pl │ ├── batch_merge.pl │ ├── batch_new.pl │ ├── batch_parse_allele_form.pl │ ├── batch_pname_update.pl │ ├── batch_split.pl │ ├── batch_variation_merge.pl │ ├── batch_variation_new.pl │ ├── batch_variations.pl │ ├── build_light.pl │ ├── bulk_annotation_update.pl │ ├── cgc_allele_parser.pl │ ├── cgc_dump.pl │ ├── cgc_strain_parser.pl │ ├── changegene.pl │ ├── check_allele_mapping.pl │ ├── check_dubious_multi_pt_2_locus.pl │ ├── check_loci_in_out_in_DfDp.pl │ ├── check_other_name_in_mapping_data.pl │ ├── fix_geneace_orthologs.pl │ ├── geneace_check.pl │ ├── geneace_patch.pl │ ├── get_EMBL_info.pl │ ├── get_EMBL_longtext.pl │ ├── get_NS_ids.pl │ ├── get_allele_flank_seq.pl │ ├── get_allele_flank_seq_multiple.pl │ ├── get_allele_flanking_seqs_TK.pl │ ├── get_gene_ids.pl │ ├── get_pi_email.pl │ ├── get_variation_ids.pl │ ├── id_resurrect.pl │ ├── incorporate_EMBL_names.pl │ ├── launch_geneace.pl │ ├── load_related_data_from_Build_to_geneace.pl │ ├── merge_variation.pl │ ├── newgene.pl │ ├── ortholog_name_transferer.pl │ ├── parse_NBP_alleles.pl │ ├── parse_Rougvie_alleles.pl │ ├── parse_allele_info_from_paper.pl │ ├── parse_cgc_name_update.pl │ ├── parse_sofa.pl │ ├── people.pl │ ├── processgene.pl │ ├── publish_gmap.pl │ ├── recent_changes.pl │ ├── remove_WBGene_from_acefile.pl │ ├── show_NS_ids.pl │ ├── showgene.pl │ ├── splitgene.pl │ ├── update_geneace.pl │ └── variation_auto_fix.pl ├── GFF_method_dump.pl ├── GFF_post_process │ ├── GFF_post_process.pl │ ├── cleanse_gff.pl │ ├── extract_canonical_geneset.pl │ ├── overload_gff_blat_species.pl │ ├── overload_gff_cds_wormpep.pl │ ├── overload_gff_gene.pl │ ├── overload_gff_genomic.pl │ ├── overload_gff_marker_positions.pl │ ├── overload_gff_mass_spec.pl │ ├── overload_gff_miRNA.pl │ ├── overload_gff_operon.pl │ ├── overload_gff_pcr_product.pl │ ├── overload_gff_rnai.pl │ ├── overload_gff_sage.pl │ ├── overload_gff_tf.pl │ ├── overload_gff_transposon.pl │ ├── overload_gff_variation.pl │ ├── post_process_gff3.pl │ ├── restructure_mirnas.pl │ └── sort_gff3.pl ├── GFFmunger.pl ├── GFFsplitter.pl ├── GeneID_updater.pl ├── GetInterPro_motifs.pl ├── GetPFAM_motifs.pl ├── KEGG.pl ├── Log_files.pm ├── MISC_SCRIPTS │ ├── atcg.pl │ ├── brugia4treefam.rb │ ├── cds2gene.pl │ ├── get_TC1_flanks.pl │ ├── get_flanking_sequences.pl │ ├── load_files_in_dir.pl │ ├── make_common_data.pl │ ├── new_genome_acedb.pl │ ├── parse_predicted_tRNA.pl │ ├── reformat_tier3_gff.pl │ ├── sequence2cds.pl │ ├── split_FASTA600k.pl │ ├── ss.pl │ ├── test.remapwig.pl │ ├── test_syntax.pl │ ├── uniquify_fasta.pl │ └── write_data_for_treefam.pl ├── Map_pos_GFFprocess.pl ├── Modules │ ├── AGR.pm │ ├── CDS.pm │ ├── CarryOver.pm │ ├── Curate.pm │ ├── EBI_datafetch.pm │ ├── Features.pm │ ├── GFF_feature.pm │ ├── Isoformer.pm │ ├── Map_Helper.pm │ ├── Overlap.pm │ ├── PWM.pm │ ├── PairedRead.pm │ ├── Physical_map.pm │ ├── RNASeq.pm │ ├── Remap_Sequence_Change.pm │ ├── SequenceObj.pm │ ├── Strand_transformer.pm │ ├── Third_party │ │ ├── LSF.pm │ │ └── LSF │ │ │ ├── Job.pm │ │ │ ├── JobGroup.pm │ │ │ ├── JobHistory.pm │ │ │ ├── JobManager.pm │ │ │ └── Queue.pm │ ├── Transcript.pm │ ├── WBSRS.pm │ ├── WormSlurm.pm │ ├── gff_model.pm │ ├── map_Alleles.pm │ └── rpkm_graph.pm ├── NAMEDB │ ├── Bio │ │ └── DB │ │ │ ├── Id.pm │ │ │ ├── Id │ │ │ ├── Domain.pm │ │ │ ├── Obj.pm │ │ │ └── ObjI.pm │ │ │ └── IdI.pm │ ├── batch_newfeature.pl │ ├── camace_nameDB_comm.pl │ ├── clonelist │ ├── geneace_nameDB_Straincomm.pl │ ├── geneace_nameDB_Varcomm.pl │ ├── geneace_nameDB_comm.pl │ ├── lib │ │ ├── NSAPI.pm │ │ ├── NameDB.pm │ │ ├── NameDBI.pm │ │ └── NameDB_handler.pm │ ├── scripts │ │ ├── Nameserver.pl │ │ ├── acdeb2nameDB.pl │ │ ├── feature_server.pl │ │ ├── id_adddomain.pl │ │ ├── id_addname.pl │ │ ├── id_addtype.pl │ │ ├── id_delname.pl │ │ ├── id_find.pl │ │ ├── id_init.pl │ │ ├── id_listdomains.pl │ │ ├── id_listtypes.pl │ │ ├── id_ls.pl │ │ ├── id_newid.pl │ │ ├── id_stat.pl │ │ ├── id_unmerge.pl │ │ ├── make_vars.txt.pl │ │ ├── nameserver_json.pl │ │ ├── test_namedb.pl │ │ └── variation_server.pl │ └── variation_server_compare.pl ├── ONTOLOGY │ ├── GAF.pm │ ├── get_easy_phenotypes.pl │ ├── make_GO_GAF.pl │ ├── make_anatomy_GAF.pl │ ├── make_disease_GAF.pl │ ├── make_lifestage_GAF.pl │ ├── make_phenotype_GAF.pl │ ├── make_phenotype_GO_GAF.pl │ ├── parse_expr_pattern_new.pl │ ├── parse_go_terms_new.pl │ ├── parse_phenotype_new.pl │ └── update_GO_terms.pl ├── Overlap.pl ├── PCR_product2Genome.pl ├── PFAM_active_sites.pl ├── ProteinConsequence │ ├── BaseProteinConsequence.pm │ ├── CollateData.pm │ ├── CreateAce.pm │ ├── InitJobs.pm │ ├── MapVariation.pm │ ├── ProteinConsequence_conf.pm │ ├── RunPartialVep.pm │ └── RunVep.pm ├── RNASeq_Study.ini_update.pl ├── RNASeq_align.pl ├── RNASeq_align_job.pl ├── RNASeq_determine_strandedness.pl ├── RNASeq_edit_config_files.pl ├── RNASeq_find_TSL.pl ├── RNASeq_intron_parser.pl ├── RNASeq_make_analysis_objects.pl ├── RNASeq_status.pl ├── RNASeq_update_config_files.pl ├── RNAi2Genome.pl ├── RNAseq │ ├── calc_RPKM.pl │ ├── genes_by_lifestage.pl │ └── run_exonerate.pl ├── Sequence_extract.pm ├── Species.pm ├── TESTS │ ├── CarryOver.pl │ └── coords_converter.t ├── TSLcheck.pl ├── TextANSIColor.pm ├── TransferDB.pl ├── Transposon_sync.pl ├── WBGene_span.pl ├── Wormbase.pm ├── Wormtest.pm ├── acecompress.pl ├── acediff.pl ├── acezip.pl ├── add_info_to_MassSpec_GFF.pl ├── add_species_to_BLAT_GFF.pl ├── agp2dna.pl ├── agp2fpc.pl ├── archive_builddir.pl ├── assign_orientation.pl ├── attach_other_nematode_ests.pl ├── autoace_builder.pl ├── batch_transcript_build.pl ├── blat2ace.pl ├── blat2bed.pl ├── blat_them_all.pl ├── build_dumpGFF.pl ├── build_pepace.pl ├── build_release_files.pl ├── bulk_history_maker.pl ├── camcheck.pl ├── changed_swissprot_proteins.pl ├── check4bigstuff.pl ├── checkLongText.pl ├── check_CDS_tace.pm ├── check_DNA.pl ├── check_EMBL_submissions.pl ├── check_PCR_products ├── check_class.pl ├── check_class_tags.pl ├── check_loci_in_out_in_DfDp.pl ├── check_other_name_in_mapping_data.pl ├── check_predicted_genes.pl ├── check_primary_database.pl ├── check_protein_ID.pl ├── check_sequence_inheritance.pl ├── check_split_camaces.pl ├── check_superlinks.pl ├── chromosome_dump.pl ├── clean_up_cmid ├── cleanup_FTP_site.pl ├── clustal_runner.pl ├── cluster_gene_connection.pl ├── collapse_redundant_probes.pl ├── compare_ena_submissions.pl ├── composition ├── confirm_genes.pl ├── coords_lookup.pl ├── correlate_Protein_IDs.pl ├── count_confirmed_intron_in_CDS.pl ├── create_PMCIDs.pl ├── create_ortholog_flatfiles.pl ├── cufflinks2ace.pl ├── curate.pl ├── current_DB_check.pl ├── data_checks.pl ├── database_checks.pl ├── datomic_check_classes.pl ├── db_backup_and_compare.pl ├── dbcomp.pl ├── dbfetch.pl ├── delete_EMBL_DNA_protein_seqs.pl ├── download_human_IPI.pl ├── dump_citindex.pl ├── dump_clustal.tcsh ├── dump_gff_batch.pl ├── dump_ko.pl ├── dump_primary_seq_data.pl ├── dumpace ├── embl2ace ├── emblpid2ace.pl ├── estcheck ├── expression_data_from_tiling_array.pl ├── fasta2samelength_0.2 ├── fasta_dumper.pl ├── fetch_EMBL_seqs_for_blatting.pl ├── fetch_seqs_for_blatting.pl ├── find_anomalies.pl ├── find_intergenic.pl ├── find_match.pl ├── find_short_genes.pl ├── find_upstream_seqs.pl ├── find_utrs.pl ├── finish_build.pl ├── fix_interpolation.pl ├── flipper ├── forum_check.pl ├── fpc2staticgp.pl ├── further_BLAST_dump.pl ├── genbank_contigs_2_ace.pl ├── genefinder2ace.pl ├── geneprediction_utility_scripts │ ├── bed_ncrna2ace.pl │ ├── bed_pseudogene2ace.pl │ ├── cds2transcripts.pl │ ├── cufflinks2ace.pl │ ├── dump_gff.pl │ ├── exonerate2ace.pl │ ├── fix_gene_spans.pl │ ├── move_cgc_name.pl │ ├── operon_miner.pl │ └── rename_cds.pl ├── generate_OMIM_xref.pl ├── generate_RRID_data.pl ├── generate_dbxref_file.pl ├── generate_disease_class.pl ├── generate_gff_report.pl ├── genestats.pl ├── genome-changes.pl ├── getProteinID.pl ├── getSwissTrembldata.pl ├── get_CRC64_checksum.pl ├── get_EMBL_data.pl ├── get_EMBL_info.pl ├── get_EMBL_longtext.pl ├── get_GI.pl ├── get_TSL_RNASeq_reads.pl ├── get_changed_cgc_names.pl ├── get_chromosome.pl ├── get_clone_sizes.pl ├── get_ena_submission_xrefs.pl ├── get_flanking_sequences.pl ├── get_flanking_sequences_simple.pl ├── get_gene_ids_ebiprod.pl ├── get_overlap_right ├── get_pfam.pl ├── get_protein_ids_ebiprod.pl ├── get_protein_xrefs.pl ├── get_repeatmasked_chroms.pl ├── get_sequence_versions_ebiprod.pl ├── get_sequences_gff.pl ├── get_treefam.pl ├── get_wormpep_annotations_from_swiss_prot ├── gf2ace ├── gff2feature_data.pl ├── gff3ace.pl ├── gff_sort ├── gfprep ├── grepace.pl ├── group_gff_entities.pl ├── history_maker.pl ├── hmmfs2ace2 ├── hmmfs2ace2_4 ├── ignore_bad_blat_alignments.pl ├── inherit_GO_terms.pl ├── initiate_build.pl ├── inspect-old-releases.pl ├── interpolate_gff.pl ├── interpolation_manager.pl ├── intersect_gff.pl ├── introncheck ├── isoformer.pl ├── landmark_genes2gff.pl ├── load2database.pl ├── load_anomalies.pl ├── load_anomalies_gff_file.pl ├── load_blat2db.pl ├── load_data_sets.pl ├── load_interpolated_map.pl ├── load_panther_xrefs.pl ├── load_refseq_xrefs.pl ├── load_uniprot_brief_ids.pl ├── lsfsubmit.pl ├── makeChromLinks.pl ├── make_EMBL_unfinished.pl ├── make_FTP_sites.pl ├── make_GTF_transcript.pl ├── make_Interpro2GO_mapping.pl ├── make_UTR_GFF.pl ├── make_acefiles.pl ├── make_agp_file.pl ├── make_assembly_manifest.pl ├── make_autoace.pl ├── make_bam_xml.pl ├── make_current.embl ├── make_enhancer_features.pl ├── make_isoforms.pl ├── make_keysets.pl ├── make_life_stage_expression.pl ├── make_mass_spec_ace.pl ├── make_missing_tsl_features.pl ├── make_oligo_set_mapping_table.pl ├── make_pseudo_map_positions.pl ├── make_wormpep.pl ├── make_wormrna.pl ├── makechromosomes.pl ├── makesuperlinks ├── makesuperlinks.pl ├── map_Alleles.pl ├── map_Interaction.pl ├── map_Oligo_set.pl ├── map_PCR_products.pl ├── map_RNAi.pl ├── map_Y2H.pl ├── map_feature2gene.pl ├── map_features.pl ├── map_microarray.pl ├── map_nematode_contigs.pl ├── map_operons.pl ├── map_tags.pl ├── map_tec-reds.pl ├── md5check.pl ├── merge_all_species.pl ├── merge_split_camaces.pl ├── merge_split_geneace.pl ├── misc │ ├── batch_genefind.pl │ ├── check_homol_size.pl │ ├── converter_servlet.rb │ ├── genefinder.pl │ ├── generate_files_for_UCSC.pl │ ├── get_splice_flanks.pl │ ├── split_blastx_by_centre.pl │ └── splitgene_brig.pl ├── molecular_names_for_genes.pl ├── move_schild_to_top_level.pl ├── new_wormpep_entries.pl ├── newembl2ace ├── next_builder_checks.pl ├── object_count.pl ├── oligo_del.test ├── ortholog │ ├── eggnog.rb │ ├── inparanoid8.rb │ ├── inparanoid8other.rb │ ├── ladeanna.rb │ ├── oma2ace.rb │ ├── ortho_mcl.rb │ └── panther_hs.pl ├── overlapcheck.pl ├── p2msql.pl ├── parse_SO_obo.pl ├── parse_flatfile.pl ├── parse_history.pl ├── parse_sofa.pl ├── pfetch_gene ├── pfscanpdb ├── pk_to_EMBL.pl ├── populate_genome_spreadsheet.pl ├── pos.pl ├── post_build_checks.pl ├── preFTPdumps │ ├── generic │ │ └── dump_resource_laboratory_designations.pl │ └── perSpecies │ │ ├── Dumper.pm │ │ ├── chunk_dump_promoters.pl │ │ ├── dump_alaska_ids.pl │ │ ├── dump_cdna2orf.pl │ │ ├── dump_confirmed_genes.pl │ │ ├── dump_geneid_list.pl │ │ ├── dump_gpi.pl │ │ ├── dump_gpiv2.pl │ │ ├── dump_interpolated.pl │ │ ├── dump_ko.pl │ │ ├── dump_molecules.pl │ │ ├── dump_pcr_list.pl │ │ ├── dump_promoters.pl │ │ ├── dump_protein_domains.pl │ │ ├── dump_species_functional_descriptions.pl │ │ ├── dump_species_gene_interactions.pl │ │ ├── dump_species_orthologs.pl │ │ ├── dump_swissprot.pl │ │ ├── pre_ftp_dumps.pl │ │ └── uniprotxrefs.pl ├── prepare_DBXREF_data.pl ├── prepare_primary_databases.pl ├── processGFF.pl ├── process_other_ESTs.rb ├── process_sage_gff.pl ├── promote_omim_data.pl ├── promote_protein_xrefs_to_gene.pl ├── propagate_cds_xrefs_to_protein.pl ├── protein_multiple_alignments.pl ├── queryprosite ├── quick_gff_dump.pl ├── reformat_acediff ├── release_letter.pl ├── remap_chromosome_homol_data.pl ├── remap_clone_feature_data.pl ├── remap_clone_homol_data.pl ├── remap_expression.pl ├── remap_fosmids_between_releases.pl ├── remap_genefinder_between_releases.pl ├── remap_gff_between_releases.pl ├── remap_mass_spec_between_releases.pl ├── remap_twinscan_between_releases.pl ├── remap_variation_gff_between_releases.pl ├── remap_wig.pl ├── remove_unwanted_GFF_lines.pl ├── reorder_exons.pl ├── repeatmasker2ace.pl ├── rewrap ├── rnai2genome_standalone.pl ├── rnaseq.pl ├── rnaseq_assign_strand.pl ├── rollback.pl ├── run_build_tests.pl ├── run_genefinder.pl ├── run_inverted.pl ├── run_vep_pipeline.pl ├── script_template.pl ├── shatter ├── shatter.pl ├── sjj_rnai_mapping_standalone.pl ├── slurm_submit.pl ├── split_alleles.pl ├── submit_TO_SUBMIT_contents ├── test_remap_between_releases.pl ├── tier3_stubs.pl ├── tkcurate.pl ├── track_protein_history.pl ├── transcript_builder.pl ├── transcriptmasker.pl ├── transfer_interpro_GO_terms.pl ├── treefam │ ├── check_reverse.rb │ ├── dump_treefam.rb │ ├── fix_treefam_from_ace.pl │ ├── treefam_orthologs.pl │ └── treefam_other_orthologs.pl ├── unpack_db.pl ├── update_Common_data.pl ├── update_feature_targets.pl ├── update_gffdb.csh ├── update_inferred_multi_pt.pl ├── update_live_release.pl ├── update_model.pl ├── update_person.pl ├── update_rev_physicals.pl ├── update_web_gene_names.pl ├── upload_empc_links.pl ├── web_data │ ├── add_elegans_aliases_to_gff.pl │ ├── build_webdb.pl │ ├── dump_protein_features_gff.pl │ ├── interpolate_gmap2pmap.pl │ ├── make_web_blast.pl │ ├── map_translated_features_to_genome.pl │ ├── maria_build.cnf │ └── process_elegans_gff-standalone.pl ├── wee_gff_dump ├── what_seq_id_is_next.pl ├── workload.pl ├── wormBLAST.pl └── write_DB_remark.pl ├── wgf ├── cds.hex ├── newnem.atg ├── newnem.codon ├── newnem.gene ├── newnem.intron3 ├── newnem.intron3_old ├── newnem.intron5 ├── newnem.intron5_old ├── ref.hist ├── tables ├── zk637.atg ├── zk637.intron3 ├── zk637.intron5 └── zk637.trinuc ├── wquery ├── BLASTX_data.def ├── CDS2proteinID.def ├── CDSlist.def ├── CDSs_with_multiple_genes.def ├── CommonData:CDS2wormpep ├── CommonData:CDS_CGCname.def ├── CommonData:CDS_Lab.def ├── CommonData:CDS_Status.def ├── CommonData:CDS_proteinID.def ├── CommonData:Clone_Accession.def ├── CommonData:Clone_Lab.def ├── CommonData:Clone_SequenceVersion.def ├── CommonData:Clone_Size_briggsae.def ├── CommonData:Clone_Size_elegans.def ├── CommonData:Clone_Type.def ├── CommonData:EST_Feature.def ├── CommonData:EST_data.def ├── CommonData:Pseudogene_CGCname.def ├── CommonData:Pseudogene_Lab.def ├── CommonData:RNA_BriefID.def ├── CommonData:RNA_CGCname.def ├── CommonData:RNAgene_Lab.def ├── CommonData:WormGene_CGCname.def ├── CommonData:WormGene_GeneID.def ├── CommonData:clone2dbid.def ├── DNA_homols.def ├── EST2feature.def ├── EST_clone.def ├── EST_data.def ├── EST_match.def ├── ESTacc2names.def ├── ESTnames.def ├── ESTnoacc.def ├── ESTorient.def ├── GI_number.def ├── No_of_tm_domains.def ├── PCRoverlap.def ├── RNAgene2lab.def ├── RNAi_dna.def ├── SCRIPT:CDS_status.def ├── SCRIPT:GeneGO_codes.def ├── SCRIPT:GeneID_updater.pl.def ├── SCRIPT:HXcds2protID.def ├── SCRIPT:UCSC_browser_files.def ├── SCRIPT:UCSC_browser_files_nc.def ├── SCRIPT:camace_nameDB_comm.def ├── SCRIPT:check_EMBL_submissions.def ├── SCRIPT:estfetch.def ├── SCRIPT:geneace_nameDB_comm.def ├── SCRIPT:inherit_GO_terms.def ├── SCRIPT:make_wormpep.def ├── SCRIPT:omim.def ├── SCRIPT:operon.def ├── SCRIPT:transcriptmasker.def ├── WBGene2seq.def ├── WBperson_first_middle_last_names.def ├── accession2clone.def ├── allele2clone.def ├── allele_designation_to_LAB.def ├── allele_has_seq.def ├── allele_to_gene_id.def ├── allele_to_locus.def ├── author.paper.def ├── cDNA2CDS.def ├── cDNA_CDS_EST5_EST3_METHOD.def ├── cDNA_CDS_EST_5_EST_3.def ├── cDNApairs.def ├── cds2lab.def ├── cds_est.def ├── cgc2cds.def ├── cgc_names_for_worm_genes.def ├── clone2map.def ├── clone2sv.def ├── clone2type.def ├── clone_to_lab.def ├── clonesize.def ├── col_cosmid.def ├── cosmid.status.def ├── deleted_ESTs.def ├── df_dup_1.def ├── dl-960813.def ├── eleanor.def ├── external.parameter.def ├── feature_SL1.def ├── feature_SL2.def ├── feature_binding_site.def ├── feature_polyA_signal.def ├── feature_polyA_signal_sequence.def ├── feature_polyA_site.def ├── features.def ├── find_UTR.def ├── gene2cgc_name_and_sequence_name.def ├── gene2go.def ├── gene2molecular_name.def ├── gene2pid.def ├── gene_IDs_for_worm_genes.def ├── geneace │ ├── CGC_name_2_person_evidence.def │ ├── CGC_table-1.def │ ├── CGC_table-3_intmap.def │ ├── CGC_table-3_map.def │ ├── Gene_public_name.txt │ ├── Gene_public_names.def │ ├── REMOVED │ │ ├── 2-pt.def │ │ ├── KO_allele_flank_seqs.def │ │ ├── WBPerson_not_linked_to_lab.def │ │ ├── WBperson_and_all_names.def │ │ ├── allele_has_flankSeq_and_no_seq.def │ │ ├── allele_has_predicted_gene_and_no_seq.def │ │ ├── allele_method_has_no_isolation_tag.def │ │ ├── allele_methods.def │ │ ├── cds_locus_other_name.def │ │ ├── cds_locus_other_seq.def │ │ ├── cgc_approved_loci.def │ │ ├── dump_allele_data.def │ │ ├── lab_allele_pi_mail.def │ │ ├── lab_representative.def │ │ ├── laboratory_has_person.def │ │ ├── loci_linked-not_linked_2_pos_clone.def │ │ ├── loci_not_linked_to_seq.def │ │ ├── locus_data.def │ │ ├── locus_has_genomic_seq.def │ │ ├── locus_in_strain.def │ │ ├── locus_pseudogene.def │ │ ├── locus_seq.def │ │ ├── locus_to_Transcripts.def │ │ ├── locus_transcript.def │ │ ├── marker_gmap_of_each_chrom.def.old │ │ ├── markers_on_genetic_and_physical_maps.def │ │ ├── multi-pt.def │ │ ├── no_remark_in_geneclass_for_merged_loci.def │ │ ├── person_also_known_as.def │ │ └── pos-neg.def │ ├── SCRIPT:GeneID_updater.pl.def │ ├── SCRIPT:geneace_nameDB_comm.def │ ├── SCRIPT:operon.def │ ├── WBperson_first_middle_last_names.def │ ├── allele_designation_to_LAB.def │ ├── allele_has_seq.def │ ├── allele_to_gene_id.def │ ├── allele_to_locus.def │ ├── cgc_names_for_worm_genes.def │ ├── clone_to_lab.def │ ├── dead_merged_gene.def │ ├── dead_merged_public_name.def │ ├── gene2cgc_name_and_sequence_name.def │ ├── gene2molecular_name.def │ ├── gene_IDs_for_worm_genes.def │ ├── geneace_gene_info.def │ ├── genes_made_into_transposons.def │ ├── genome_seq_to_lab.def │ ├── get_WBPersonID_fn_ln.def │ ├── get_elegans_CDS_source_exons.def │ ├── get_elegans_RNA_gene_source_exons.def │ ├── get_overlapped_clones.def │ ├── locus_2_gmap.def │ ├── rearr_L_R_ends.def │ ├── strain_genotype.def │ ├── transgene_ids.def │ └── variation_nameserver_comm.def ├── geneace_gene_info.def ├── genelist.def ├── genes_without_evidence.def ├── get_CDS_to_gene.def ├── get_WBPersonID_fn_ln.def ├── get_predicted_gene_to_locus.def ├── get_pseudogene_to_gene.def ├── get_transcript_to_gene.def ├── id2clone.def ├── idandacc2clone.def ├── intron.def ├── journal.def ├── locus_sts_multi_map.def ├── map2homology.def ├── map_data.def ├── marker_gmap_of_each_chrom.def ├── methods.def ├── missing_GI_numbers.def ├── molecular_names_for_genes.def ├── new_sequences.def ├── new_wormpep.def ├── orthologs.def ├── pcr_product2gene.def ├── problem_S_children.def ├── pseudogene2lab.def ├── roughcheck.def ├── sequence_versions.def ├── strain_genotype.def ├── tRNA_info_1.def ├── tRNA_info_2.def ├── trna_with_introns.def ├── unc_genes_few_alleles.def ├── up-assembly.def ├── upsubsequences.def ├── using.author.def ├── wormfam.def ├── wormpep.def ├── wormpep.table.def ├── wormpep2.def ├── wormpepCE_DNA_Locus_OtherName.def ├── wormpep_lengths.def └── yk2ORF.def └── wspec ├── cachesize.wrm ├── constraints.wrm ├── copyright ├── database.wrm ├── displays.wrm ├── help.wrm ├── layout.wrm ├── models.wrm ├── models.wrm.NS ├── models.wrm.annot ├── options.wrm ├── passwd.wrm ├── passwd_anon.wrm ├── psfonts.wrm ├── serverconfig.wrm ├── serverpasswd.wrm ├── subclasses.wrm └── xfonts.wrm /.gitignore: -------------------------------------------------------------------------------- 1 | ._* 2 | parasite/scripts/production/core-creation/ensembl 3 | parasite/scripts/production/ncbi/tmp 4 | *__pycache__/ 5 | *.pyc 6 | parasite/scripts/production/nextflow/workflows/busco_pipeline/work 7 | parasite/scripts/production/nextflow/workflows/busco_pipeline/.nextflow 8 | parasite/scripts/production/nextflow/workflows/busco_pipeline/*.log* 9 | -------------------------------------------------------------------------------- /README.txt: -------------------------------------------------------------------------------- 1 | Git Branch of the WormBase pipeline code 2 | 3 | This is the main source repository of the WormBase codebase of the Hinxton team of WormBase. 4 | The main purpose of the code is to build and process data in order to release a final database. 5 | 6 | Main Project Site: 7 | http://www.wormbase.org 8 | 9 | 10 | -------------------------------------------------------------------------------- /config/nematoda/Aphelenchoides_besseyi.ini: -------------------------------------------------------------------------------- 1 | [SRP033379] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Aphelenchoides besseyi 8 | secondary_study_accession=SRP033379 9 | study_accession=PRJNA229675 10 | study_title=Aphelenchoides besseyi Transcriptome or Gene expression 11 | center_name=Northeast Forestry University 12 | tax_id=269767 13 | Colour= 14 | study_description=Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed stage population of A. besseyi. 15 | library_selection_SRX385206=other 16 | library_sample_SRX385206=SRS509362 17 | sample_longLabel_SRS509362= 18 | sample_shortLabel_SRS509362= 19 | sample_ChEBI_ID_SRS509362= 20 | sample_WormBaseLifeStage_SRS509362= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Bursaphelenchus_mucronatus.ini: -------------------------------------------------------------------------------- 1 | [SRP008063] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Bursaphelenchus mucronatus 8 | secondary_study_accession=SRP008063 9 | study_accession=SRP008063 10 | study_title=Comparative Transcriptomes Analysis of Two Pinewood Nematodes Bursaphelenchus xylophilus and Bursaphelenchus mucronatus by Deep-Sequencing Technology 11 | center_name=Individual 12 | tax_id=6325 13 | Colour= 14 | library_selection_SRX096027=RANDOM 15 | library_sample_SRX096027=SRS259967 16 | sample_longLabel_SRS259967= 17 | sample_shortLabel_SRS259967= 18 | sample_ChEBI_ID_SRS259967= 19 | sample_WormBaseLifeStage_SRS259967= 20 | 21 | [GENERAL] 22 | general_bioproject= 23 | -------------------------------------------------------------------------------- /config/nematoda/Caenorhabditis_angaria.ini: -------------------------------------------------------------------------------- 1 | [SRP003492] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Caenorhabditis angaria 8 | secondary_study_accession=SRP003492 9 | study_accession=PRJNA51225 10 | study_title=Caenorhabditis angaria genome sequencing project 11 | center_name=Cal. Inst. of Tech., Division of Biology 12 | tax_id=860376 13 | Colour= 14 | study_description=This strain will be used for comparative genome analysis. 15 | library_selection_SRX026727=cDNA 16 | library_sample_SRX026727=SRS114803 17 | sample_longLabel_SRS114803= 18 | sample_shortLabel_SRS114803= 19 | sample_ChEBI_ID_SRS114803= 20 | sample_WormBaseLifeStage_SRS114803= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Dictyocaulus_filaria.ini: -------------------------------------------------------------------------------- 1 | [SRP032224] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Dictyocaulus filaria 8 | secondary_study_accession=SRP032224 9 | study_accession=PRJNA222411 10 | study_title=Dictyocaulus filariaTranscriptome or Gene expression 11 | center_name=Melbourne University 12 | tax_id=44603 13 | Colour= 14 | study_description=We established and used a bioinformatic workflow to compare, both qualitatively and quantitatively, the transcriptomes of the adult stages of the lungworms Dictyocaulus filaria and D. viviparus in the absence of reference genomes. 15 | library_selection_SRX368686=unspecified 16 | library_sample_SRX368686=SRS494410 17 | sample_longLabel_SRS494410= 18 | sample_shortLabel_SRS494410= 19 | sample_ChEBI_ID_SRS494410= 20 | sample_WormBaseLifeStage_SRS494410= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Enoplus_brevis.ini: -------------------------------------------------------------------------------- 1 | [ERP008507] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Enoplus brevis 8 | secondary_study_accession=ERP008507 9 | study_accession=PRJEB7588 10 | study_title=The genome and transcriptome of the marine nematode Enoplus brevis. 11 | center_name=BANG 12 | tax_id=57292 13 | Colour= 14 | study_description=The genome and transcriptome of the marine nematode Enoplus brevis. 15 | library_selection_ERX616982=RANDOM 16 | library_sample_ERX616982=ERS571105 17 | sample_longLabel_ERS571105= 18 | sample_shortLabel_ERS571105= 19 | sample_ChEBI_ID_ERS571105= 20 | sample_WormBaseLifeStage_ERS571105= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Halomonhystera_disjuncta.ini: -------------------------------------------------------------------------------- 1 | [SRP050898] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Halomonhystera disjuncta 8 | secondary_study_accession=SRP050898 9 | study_accession=PRJNA268901 10 | study_title=Halomonhystera Transcriptome or Gene expression 11 | center_name=Ghent University 12 | tax_id=535939 13 | Colour= 14 | study_description=Comparison of the transcriptome of a intertidal and deep-sea nematode to elucidate the adaptation and evolutionary to difference in relation to the environment 15 | library_selection_SRX764337=PolyA 16 | library_sample_SRX764337=SRS748703 17 | sample_longLabel_SRS748703= 18 | sample_shortLabel_SRS748703= 19 | sample_ChEBI_ID_SRS748703= 20 | sample_WormBaseLifeStage_SRS748703= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Halomonhystera_hermesi.ini: -------------------------------------------------------------------------------- 1 | [SRP050898] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Halomonhystera hermesi 8 | secondary_study_accession=SRP050898 9 | study_accession=PRJNA268901 10 | study_title=Halomonhystera Transcriptome or Gene expression 11 | center_name=Ghent University 12 | tax_id=1573192 13 | Colour= 14 | study_description=Comparison of the transcriptome of a intertidal and deep-sea nematode to elucidate the adaptation and evolutionary to difference in relation to the environment 15 | library_selection_SRX764336=PolyA 16 | library_sample_SRX764336=SRS748702 17 | sample_longLabel_SRS748702= 18 | sample_shortLabel_SRS748702= 19 | sample_ChEBI_ID_SRS748702= 20 | sample_WormBaseLifeStage_SRS748702= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Heterodera_glycines.ini: -------------------------------------------------------------------------------- 1 | [SRP070586] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Heterodera glycines 8 | secondary_study_accession=SRP070586 9 | study_accession=PRJNA312063 10 | study_title=Parasitic Nematode Glands Gene expression 11 | center_name=WUGSC 12 | tax_id=51029 13 | Colour= 14 | study_description=This project will study the genes expressed in gland cells in nematodes. 15 | library_selection_SRX1600830=unspecified 16 | library_sample_SRX1600830=SRS1310707 17 | sample_longLabel_SRS1310707= 18 | sample_shortLabel_SRS1310707= 19 | sample_ChEBI_ID_SRS1310707= 20 | sample_WormBaseLifeStage_SRS1310707= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Hirschmanniella_oryzae.ini: -------------------------------------------------------------------------------- 1 | [SRP009636] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Hirschmanniella oryzae 8 | secondary_study_accession=SRP009636 9 | study_accession=SRP009636 10 | study_title=Analysis of the transcriptome of Hirschmanniella oryzae 11 | center_name=Ghent University 12 | tax_id=362338 13 | Colour= 14 | library_selection_SRX110506=unspecified 15 | library_sample_SRX110506=SRS281726 16 | sample_longLabel_SRS281726= 17 | sample_shortLabel_SRS281726= 18 | sample_ChEBI_ID_SRS281726= 19 | sample_WormBaseLifeStage_SRS281726= 20 | 21 | [GENERAL] 22 | general_bioproject= 23 | -------------------------------------------------------------------------------- /config/nematoda/Loa_loa.ini: -------------------------------------------------------------------------------- 1 | [SRP011638] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Loa loa 8 | secondary_study_accession=SRP011638 9 | study_accession=PRJNA60555 10 | study_title=Loa loa transcriptome sequencing project 11 | center_name=BI 12 | tax_id=7209 13 | Colour= 14 | study_description=RNA was provided by Doran Fink and Thomas Nutman at NIH. Loa Loa is a filarial worm and causative agent of filariasis in humans. 15 | library_selection_SRX130438=cDNA 16 | library_sample_SRX130438=SRS301861 17 | sample_longLabel_SRS301861= 18 | sample_shortLabel_SRS301861= 19 | sample_ChEBI_ID_SRS301861= 20 | sample_WormBaseLifeStage_SRS301861= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Longidorus_elongatus.ini: -------------------------------------------------------------------------------- 1 | [ERP009400] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Longidorus elongatus 8 | secondary_study_accession=ERP009400 9 | study_accession=PRJEB8328 10 | study_title=Longidorus elongatus mixed stage RNAseq 11 | center_name=James Hutton Institute 12 | tax_id=70231 13 | Colour= 14 | study_description=A single lane of Illumina MiSeq was used to sequence a cDNA library prepared from mixed stage Longidorus elongatus with 150 base pair paired end reads. 15 | library_selection_ERX688304=RT-PCR 16 | library_sample_ERX688304=ERS647085 17 | sample_longLabel_ERS647085= 18 | sample_shortLabel_ERS647085= 19 | sample_ChEBI_ID_ERS647085= 20 | sample_WormBaseLifeStage_ERS647085= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Panagrolaimus_davidi.ini: -------------------------------------------------------------------------------- 1 | [SRP041973] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Panagrolaimus davidi 8 | secondary_study_accession=SRP041973 9 | study_accession=PRJNA247454 10 | study_title=Panagrolaimus davidi strain:CB1 Transcriptome or Gene expression 11 | center_name=British Antarctic Survey 12 | tax_id=227884 13 | Colour= 14 | study_description=RNA-seq for sequencing and assembling the transcriptome of Panagrolaimus davidi 15 | library_selection_SRX542217=PCR 16 | library_sample_SRX542217=SRS606665 17 | sample_longLabel_SRS606665= 18 | sample_shortLabel_SRS606665= 19 | sample_ChEBI_ID_SRS606665= 20 | sample_WormBaseLifeStage_SRS606665= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Pratylenchus_penetrans.ini: -------------------------------------------------------------------------------- 1 | [SRP066773] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Pratylenchus penetrans 8 | secondary_study_accession=SRP066773 9 | study_accession=PRJNA304159 10 | study_title=Pratylenchus penetrans transcriptome 11 | center_name=ARS-USDA 12 | tax_id=45929 13 | Colour= 14 | study_description=Pratylenchus penetrans is a plan-parasitic nematode infecting a wide number of host plants 15 | library_selection_SRX1453685=PolyA 16 | library_sample_SRX1453685=SRS1181350 17 | library_selection_SRX1453819=PolyA 18 | library_sample_SRX1453819=SRS1181350 19 | library_selection_SRX1453907=PolyA 20 | library_sample_SRX1453907=SRS1181350 21 | sample_longLabel_SRS1181350= 22 | sample_shortLabel_SRS1181350= 23 | sample_ChEBI_ID_SRS1181350= 24 | sample_WormBaseLifeStage_SRS1181350= 25 | 26 | [GENERAL] 27 | general_bioproject= 28 | -------------------------------------------------------------------------------- /config/nematoda/Prionchulus_punctatus.ini: -------------------------------------------------------------------------------- 1 | [ERP008503] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prionchulus punctatus 8 | secondary_study_accession=ERP008503 9 | study_accession=PRJEB7585 10 | study_title=The transcriptome of Prionchulus punctatus 11 | center_name=BANG 12 | tax_id=293874 13 | Colour= 14 | study_description=The transcriptome of Prionchulus punctatus 15 | library_selection_ERX616947=RANDOM 16 | library_sample_ERX616947=ERS570998 17 | library_selection_ERX616948=RANDOM 18 | library_sample_ERX616948=ERS570998 19 | sample_longLabel_ERS570998= 20 | sample_shortLabel_ERS570998= 21 | sample_ChEBI_ID_ERS570998= 22 | sample_WormBaseLifeStage_ERS570998= 23 | 24 | [GENERAL] 25 | general_bioproject= 26 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_britovi.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella britovi 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=45882 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX986063=unspecified 16 | library_sample_SRX986063=SRS900949 17 | sample_longLabel_SRS900949= 18 | sample_shortLabel_SRS900949= 19 | sample_ChEBI_ID_SRS900949= 20 | sample_WormBaseLifeStage_SRS900949= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_murrelli.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella murrelli 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=144512 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992249=unspecified 16 | library_sample_SRX992249=SRS906996 17 | sample_longLabel_SRS906996= 18 | sample_shortLabel_SRS906996= 19 | sample_ChEBI_ID_SRS906996= 20 | sample_WormBaseLifeStage_SRS906996= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_nativa.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella nativa 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=6335 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX986040=unspecified 16 | library_sample_SRX986040=SRS898754 17 | sample_longLabel_SRS898754= 18 | sample_shortLabel_SRS898754= 19 | sample_ChEBI_ID_SRS898754= 20 | sample_WormBaseLifeStage_SRS898754= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_nelsoni.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella nelsoni 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=6336 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992257=unspecified 16 | library_sample_SRX992257=SRS906999 17 | sample_longLabel_SRS906999= 18 | sample_shortLabel_SRS906999= 19 | sample_ChEBI_ID_SRS906999= 20 | sample_WormBaseLifeStage_SRS906999= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_papuae.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella papuae 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=268474 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX993445=unspecified 16 | library_sample_SRX993445=SRS908054 17 | sample_longLabel_SRS908054= 18 | sample_shortLabel_SRS908054= 19 | sample_ChEBI_ID_SRS908054= 20 | sample_WormBaseLifeStage_SRS908054= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_patagoniensis.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella patagoniensis 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=990121 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992269=unspecified 16 | library_sample_SRX992269=SRS907002 17 | library_selection_SRX992270=unspecified 18 | library_sample_SRX992270=SRS907002 19 | sample_longLabel_SRS907002= 20 | sample_shortLabel_SRS907002= 21 | sample_ChEBI_ID_SRS907002= 22 | sample_WormBaseLifeStage_SRS907002= 23 | 24 | [GENERAL] 25 | general_bioproject= 26 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_sp._T6.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella sp. T6 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=92179 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992253=unspecified 16 | library_sample_SRX992253=SRS906998 17 | sample_longLabel_SRS906998= 18 | sample_shortLabel_SRS906998= 19 | sample_ChEBI_ID_SRS906998= 20 | sample_WormBaseLifeStage_SRS906998= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_sp._T8.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella sp. T8 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=92180 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992261=unspecified 16 | library_sample_SRX992261=SRS907000 17 | sample_longLabel_SRS907000= 18 | sample_shortLabel_SRS907000= 19 | sample_ChEBI_ID_SRS907000= 20 | sample_WormBaseLifeStage_SRS907000= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_sp._T9.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella sp. T9 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=181606 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992266=unspecified 16 | library_sample_SRX992266=SRS907001 17 | sample_longLabel_SRS907001= 18 | sample_shortLabel_SRS907001= 19 | sample_ChEBI_ID_SRS907001= 20 | sample_WormBaseLifeStage_SRS907001= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/nematoda/Trichinella_zimbabwensis.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella zimbabwensis 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=268475 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX993449=unspecified 16 | library_sample_SRX993449=SRS908055 17 | sample_longLabel_SRS908055= 18 | sample_shortLabel_SRS908055= 19 | sample_ChEBI_ID_SRS908055= 20 | sample_WormBaseLifeStage_SRS908055= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Bdellocephala_annandalei.ini: -------------------------------------------------------------------------------- 1 | [DRP001311] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Bdellocephala annandalei 8 | secondary_study_accession=DRP001311 9 | study_accession=PRJDB1529 10 | study_title=Transcriptome analysis of Bdellocephala annandalei 11 | center_name=NAGAHAMA_BIO 12 | tax_id=1421413 13 | Colour= 14 | study_description=To find out the change of gene expression of B. annandalei under low-oxygen conditions 15 | library_selection_DRX013308=unspecified 16 | library_sample_DRX013308=DRS013071 17 | sample_longLabel_DRS013071= 18 | sample_shortLabel_DRS013071= 19 | sample_ChEBI_ID_DRS013071= 20 | sample_WormBaseLifeStage_DRS013071= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Bdelloura_candida.ini: -------------------------------------------------------------------------------- 1 | [SRP057226] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Bdelloura candida 8 | secondary_study_accession=SRP057226 9 | study_accession=PRJNA277606 10 | study_title=Bdelloura candida Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=46766 13 | Colour= 14 | study_description=This is a cDNA library prepared from a single individual using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX997151=PolyA 16 | library_sample_SRX997151=SRS911385 17 | sample_longLabel_SRS911385= 18 | sample_shortLabel_SRS911385= 19 | sample_ChEBI_ID_SRS911385= 20 | sample_WormBaseLifeStage_SRS911385= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Catenula_lemnae.ini: -------------------------------------------------------------------------------- 1 | [SRP053430] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Catenula lemnae 8 | secondary_study_accession=SRP053430 9 | study_accession=PRJNA274961 10 | study_title=Catenula lemnae Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=570249 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Catenula lemnae 15 | library_selection_SRX871445=unspecified 16 | library_sample_SRX871445=SRS842088 17 | sample_longLabel_SRS842088= 18 | sample_shortLabel_SRS842088= 19 | sample_ChEBI_ID_SRS842088= 20 | sample_WormBaseLifeStage_SRS842088= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Echinoplana_celerrima.ini: -------------------------------------------------------------------------------- 1 | [SRP053432] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Echinoplana celerrima 8 | secondary_study_accession=SRP053432 9 | study_accession=PRJNA274964 10 | study_title=Echinoplana celerrima Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=983673 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Echinoplana celerrima 15 | library_selection_SRX871508=unspecified 16 | library_sample_SRX871508=SRS842092 17 | sample_longLabel_SRS842092= 18 | sample_shortLabel_SRS842092= 19 | sample_ChEBI_ID_SRS842092= 20 | sample_WormBaseLifeStage_SRS842092= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Fascioloides_magna.ini: -------------------------------------------------------------------------------- 1 | [SRP013117] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Fascioloides magna 8 | secondary_study_accession=SRP013117 9 | study_accession=SRP013117 10 | study_title=A deep exploration of the transcriptome and ‘excretory/secretory’ proteome of adult Fascioloides magna 11 | center_name=The University of Melbourne 12 | tax_id=394415 13 | Colour= 14 | library_selection_SRX147910=RANDOM 15 | library_sample_SRX147910=SRS333832 16 | sample_longLabel_SRS333832= 17 | sample_shortLabel_SRS333832= 18 | sample_ChEBI_ID_SRS333832= 19 | sample_WormBaseLifeStage_SRS333832= 20 | 21 | [GENERAL] 22 | general_bioproject= 23 | -------------------------------------------------------------------------------- /config/platyhelminthes/Geocentrophora_sphyrocephala.ini: -------------------------------------------------------------------------------- 1 | [SRP053435] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Geocentrophora sphyrocephala 8 | secondary_study_accession=SRP053435 9 | study_accession=PRJNA275047 10 | study_title=Geocentrophora sphyrocephala Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=6176 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Geocentrophora sphyrocephala 15 | library_selection_SRX871533=unspecified 16 | library_sample_SRX871533=SRS842123 17 | sample_longLabel_SRS842123= 18 | sample_shortLabel_SRS842123= 19 | sample_ChEBI_ID_SRS842123= 20 | sample_WormBaseLifeStage_SRS842123= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Girardia.ini: -------------------------------------------------------------------------------- 1 | [SRP070966] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Girardia 8 | secondary_study_accession=SRP070966 9 | study_accession=PRJNA313460 10 | study_title=Girardia sp Transcriptome or Gene expression 11 | center_name=SUB1364667 12 | tax_id=52316 13 | Colour= 14 | study_description=Giardia sp. Transcriptome 15 | library_selection_SRX1605771=unspecified 16 | library_sample_SRX1605771=SRS1315406 17 | sample_longLabel_SRS1315406= 18 | sample_shortLabel_SRS1315406= 19 | sample_ChEBI_ID_SRS1315406= 20 | sample_WormBaseLifeStage_SRS1315406= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Itaspiella_helgolandica.ini: -------------------------------------------------------------------------------- 1 | [SRP053637] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Itaspiella helgolandica 8 | secondary_study_accession=SRP053637 9 | study_accession=PRJNA275050 10 | study_title=Itaspiella helgolandica Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1611829 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Itaspiella helgolandica 15 | library_selection_SRX872314=unspecified 16 | library_sample_SRX872314=SRS842635 17 | sample_longLabel_SRS842635= 18 | sample_shortLabel_SRS842635= 19 | sample_ChEBI_ID_SRS842635= 20 | sample_WormBaseLifeStage_SRS842635= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Lehardyia_sp._CEL-2015.ini: -------------------------------------------------------------------------------- 1 | [SRP057525] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Lehardyia sp. CEL-2015 8 | secondary_study_accession=SRP057525 9 | study_accession=PRJNA277603 10 | study_title=Lehardyia sp. CEL-2015 Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628667 13 | Colour= 14 | study_description=This is a cDNA library prepared from a single individual using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX997426=PolyA 16 | library_sample_SRX997426=SRS916819 17 | sample_longLabel_SRS916819= 18 | sample_shortLabel_SRS916819= 19 | sample_ChEBI_ID_SRS916819= 20 | sample_WormBaseLifeStage_SRS916819= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Leptoplana_tremellaris.ini: -------------------------------------------------------------------------------- 1 | [SRP053639] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Leptoplana tremellaris 8 | secondary_study_accession=SRP053639 9 | study_accession=PRJNA275053 10 | study_title=Leptoplana tremellaris Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=107733 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Leptoplana tremellaris 15 | library_selection_SRX872321=unspecified 16 | library_sample_SRX872321=SRS842637 17 | sample_longLabel_SRS842637= 18 | sample_shortLabel_SRS842637= 19 | sample_ChEBI_ID_SRS842637= 20 | sample_WormBaseLifeStage_SRS842637= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Maritigrella_crozieri.ini: -------------------------------------------------------------------------------- 1 | [SRP054950] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Maritigrella crozieri 8 | secondary_study_accession=SRP054950 9 | study_accession=PRJNA275060 10 | study_title=Maritigrella crozieri Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=526434 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Maritigrella crozieri 15 | library_selection_SRX875739=unspecified 16 | library_sample_SRX875739=SRS844631 17 | library_selection_SRX875742=unspecified 18 | library_sample_SRX875742=SRS844631 19 | sample_longLabel_SRS844631= 20 | sample_shortLabel_SRS844631= 21 | sample_ChEBI_ID_SRS844631= 22 | sample_WormBaseLifeStage_SRS844631= 23 | 24 | [GENERAL] 25 | general_bioproject= 26 | -------------------------------------------------------------------------------- /config/platyhelminthes/Mesostoma_lingua.ini: -------------------------------------------------------------------------------- 1 | [SRP053647] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Mesostoma lingua 8 | secondary_study_accession=SRP053647 9 | study_accession=PRJNA275061 10 | study_title=Mesostoma lingua Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=99405 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Mesostoma lingua 15 | library_selection_SRX872347=unspecified 16 | library_sample_SRX872347=SRS842663 17 | sample_longLabel_SRS842663= 18 | sample_shortLabel_SRS842663= 19 | sample_ChEBI_ID_SRS842663= 20 | sample_WormBaseLifeStage_SRS842663= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Microdalyellia_fusca.ini: -------------------------------------------------------------------------------- 1 | [SRP053651] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Microdalyellia fusca 8 | secondary_study_accession=SRP053651 9 | study_accession=PRJNA275064 10 | study_title=Microdalyellia fusca Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1311901 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Microdalyellia fusca 15 | library_selection_SRX872356=unspecified 16 | library_sample_SRX872356=SRS842668 17 | sample_longLabel_SRS842668= 18 | sample_shortLabel_SRS842668= 19 | sample_ChEBI_ID_SRS842668= 20 | sample_WormBaseLifeStage_SRS842668= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Microdalyellia_schmidti.ini: -------------------------------------------------------------------------------- 1 | [SRP053655] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Microdalyellia schmidti 8 | secondary_study_accession=SRP053655 9 | study_accession=PRJNA275065 10 | study_title=Microdalyellia schmidti Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1611830 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Microdalyellia schmidti 15 | library_selection_SRX872362=unspecified 16 | library_sample_SRX872362=SRS842672 17 | sample_longLabel_SRS842672= 18 | sample_shortLabel_SRS842672= 19 | sample_ChEBI_ID_SRS842672= 20 | sample_WormBaseLifeStage_SRS842672= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Microdalyellia_sp._CEL-2015.ini: -------------------------------------------------------------------------------- 1 | [SRP057447] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Microdalyellia sp. CEL-2015 8 | secondary_study_accession=SRP057447 9 | study_accession=PRJNA277602 10 | study_title=Microdalyellia sp. CEL-2015 Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628671 13 | Colour= 14 | study_description=This is a cDNA library prepared from a single individual using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX998816=PolyA 16 | library_sample_SRX998816=SRS914130 17 | sample_longLabel_SRS914130= 18 | sample_shortLabel_SRS914130= 19 | sample_ChEBI_ID_SRS914130= 20 | sample_WormBaseLifeStage_SRS914130= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Monocelis_sp._BE-2015.ini: -------------------------------------------------------------------------------- 1 | [SRP055136] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Monocelis sp. BE-2015 8 | secondary_study_accession=SRP055136 9 | study_accession=PRJNA275067 10 | study_title=Monocelis sp. BE-2015 Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1597771 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Monocelis sp. 15 | library_selection_SRX883021=unspecified 16 | library_sample_SRX883021=SRS850388 17 | sample_longLabel_SRS850388= 18 | sample_shortLabel_SRS850388= 19 | sample_ChEBI_ID_SRS850388= 20 | sample_WormBaseLifeStage_SRS850388= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Paragonimus_skrjabini.ini: -------------------------------------------------------------------------------- 1 | [SRP067887] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Paragonimus skrjabini 8 | secondary_study_accession=SRP067887 9 | study_accession=PRJNA301597 10 | study_title=Paragonimus skrjabini Transcriptome or Gene expression 11 | center_name=WUGSC 12 | tax_id=59630 13 | Colour= 14 | study_description=The human lung fluke Paragonimus skrjabini represents one of the food-borne helminths infecting humans. These flukes cause paragonimiasis in people and other crab-eating mammals primarily in Asia. 15 | library_selection_SRX1507709=unspecified 16 | library_sample_SRX1507709=SRS1228562 17 | sample_longLabel_SRS1228562= 18 | sample_shortLabel_SRS1228562= 19 | sample_ChEBI_ID_SRS1228562= 20 | sample_WormBaseLifeStage_SRS1228562= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Phagocata_gracilis.ini: -------------------------------------------------------------------------------- 1 | [SRP070949] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Phagocata gracilis 8 | secondary_study_accession=SRP070949 9 | study_accession=PRJNA312785 10 | study_title=Phagocata gracilis Transcriptome or Gene expression 11 | center_name=SUB1353050 12 | tax_id=1354672 13 | Colour= 14 | study_description=Phagocata gracilis Transcriptome 15 | library_selection_SRX1605188=unspecified 16 | library_sample_SRX1605188=SRS1314900 17 | sample_longLabel_SRS1314900= 18 | sample_shortLabel_SRS1314900= 19 | sample_ChEBI_ID_SRS1314900= 20 | sample_WormBaseLifeStage_SRS1314900= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Phagocata_morgani.ini: -------------------------------------------------------------------------------- 1 | [GENERAL] 2 | general_bioproject= 3 | 4 | [SRP072346] 5 | use= 6 | remark= 7 | pubmed= 8 | status= 9 | ArrayExpress_ID= 10 | scientific_name=Phagocata morgani 11 | secondary_study_accession=SRP072346 12 | study_accession=PRJNA316133 13 | study_title=Phagocata morgani Transcriptome or Gene expression 14 | center_name=SUB1404679 15 | tax_id=1820202 16 | Colour= 17 | study_description="white planaria" from Carolina Biological Supply 18 | library_selection_SRX1661675=RANDOM 19 | library_sample_SRX1661675=SRS1361318 20 | sample_longLabel_SRS1361318= 21 | sample_shortLabel_SRS1361318= 22 | sample_ChEBI_ID_SRS1361318= 23 | sample_WormBaseLifeStage_SRS1361318= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Prosogynopora_riseri.ini: -------------------------------------------------------------------------------- 1 | [SRP057523] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prosogynopora riseri 8 | secondary_study_accession=SRP057523 9 | study_accession=PRJNA277597 10 | study_title=Prosogynopora riseri Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628673 13 | Colour= 14 | study_description=This is a cDNA library prepared from a single individual using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX998821=PolyA 16 | library_sample_SRX998821=SRS916817 17 | sample_longLabel_SRS916817= 18 | sample_shortLabel_SRS916817= 19 | sample_ChEBI_ID_SRS916817= 20 | sample_WormBaseLifeStage_SRS916817= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Prostheceraeus_vittatus.ini: -------------------------------------------------------------------------------- 1 | [SRP057407] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prostheceraeus vittatus 8 | secondary_study_accession=SRP057407 9 | study_accession=PRJNA277637 10 | study_title=Prostheceraeus vittatus Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=107736 13 | Colour= 14 | study_description=This is a cDNA library that was constructed using adult and embryological material pooled prior to RNA extraction, using the Illumina TruSeq v2 RNA protocol, and sequenced on a full lane of an Illumina HiSeq 2000. 15 | library_selection_SRX999630=PolyA 16 | library_sample_SRX999630=SRS913668 17 | sample_longLabel_SRS913668= 18 | sample_shortLabel_SRS913668= 19 | sample_ChEBI_ID_SRS913668= 20 | sample_WormBaseLifeStage_SRS913668= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Prosthiostomum_siphunculus.ini: -------------------------------------------------------------------------------- 1 | [SRP053679] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prosthiostomum siphunculus 8 | secondary_study_accession=SRP053679 9 | study_accession=PRJNA275073 10 | study_title=Prosthiostomum siphunculus Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=983679 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Prosthiostomum siphunculus 15 | library_selection_SRX872403=unspecified 16 | library_sample_SRX872403=SRS842699 17 | sample_longLabel_SRS842699= 18 | sample_shortLabel_SRS842699= 19 | sample_ChEBI_ID_SRS842699= 20 | sample_WormBaseLifeStage_SRS842699= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Rhynchomesostoma_rostratum.ini: -------------------------------------------------------------------------------- 1 | [SRP057392] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Rhynchomesostoma rostratum 8 | secondary_study_accession=SRP057392 9 | study_accession=PRJNA277594 10 | study_title=Rhynchomesostoma rostratum Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1311950 13 | Colour= 14 | study_description=This is a stranded cDNA library prepared from two adults pooled prior to RNA extraction, using the Apollo324 (IntegenX, now WaferGen) PrepX mRNA protocol, and sequenced in multiplex 2x100 bp on an Illumina HiSeq 2000. 15 | library_selection_SRX999311=PolyA 16 | library_sample_SRX999311=SRS913342 17 | sample_longLabel_SRS913342= 18 | sample_shortLabel_SRS913342= 19 | sample_ChEBI_ID_SRS913342= 20 | sample_WormBaseLifeStage_SRS913342= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Stenostomum_sthenum.ini: -------------------------------------------------------------------------------- 1 | [SRP053680] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Stenostomum sthenum 8 | secondary_study_accession=SRP053680 9 | study_accession=PRJNA275074 10 | study_title=Stenostomum sthenum Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1611831 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Stenostomum sthenum 15 | library_selection_SRX872404=unspecified 16 | library_sample_SRX872404=SRS842700 17 | sample_longLabel_SRS842700= 18 | sample_shortLabel_SRS842700= 19 | sample_ChEBI_ID_SRS842700= 20 | sample_WormBaseLifeStage_SRS842700= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Taenia_asiatica.ini: -------------------------------------------------------------------------------- 1 | [GENERAL] 2 | general_bioproject= 3 | 4 | [SRP065637] 5 | use= 6 | remark= 7 | pubmed= 8 | status= 9 | ArrayExpress_ID= 10 | scientific_name=Taenia asiatica 11 | secondary_study_accession=SRP065637 12 | study_accession=PRJNA299871 13 | study_title=Taenia asiatica genome sequencing 14 | center_name=Beijing Institute of Genomics, Chinese Academy of 15 | tax_id=60517 16 | Colour= 17 | study_description=We expect to obtain Asian tapeworm genome and analyze genomic features. 18 | library_selection_SRX1410253=RANDOM 19 | library_sample_SRX1410253=SRS1144730 20 | sample_longLabel_SRS1144730= 21 | sample_shortLabel_SRS1144730= 22 | sample_ChEBI_ID_SRS1144730= 23 | sample_WormBaseLifeStage_SRS1144730= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Taenia_crassiceps.ini: -------------------------------------------------------------------------------- 1 | [SRP014613] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Taenia crassiceps 8 | secondary_study_accession=SRP014613 9 | study_accession=PRJNA171338 10 | study_title=Taenia crassiceps strain:ORF Transcriptome or Gene expression 11 | center_name=Universidad de Antioquia 12 | tax_id=6207 13 | Colour= 14 | study_description=Transcriptome analysis of the cysticercus stage of the cestode Taenia crassiceps. mRNA was purified and 454 sequenced. 15 | library_selection_SRX171519=RANDOM 16 | library_sample_SRX171519=SRS352306 17 | sample_longLabel_SRS352306= 18 | sample_shortLabel_SRS352306= 19 | sample_ChEBI_ID_SRS352306= 20 | sample_WormBaseLifeStage_SRS352306= 21 | 22 | [GENERAL] 23 | general_bioproject= 24 | -------------------------------------------------------------------------------- /config/platyhelminthes/Taenia_pisiformis.ini: -------------------------------------------------------------------------------- 1 | [SRP006907] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Taenia pisiformis 8 | secondary_study_accession=SRP006907 9 | study_accession=SRP006907 10 | study_title=De novo assembly and analysis of high sequencing-based transcriptome data of Taenia pisiformis 11 | center_name=Sichuan Agriculture University 12 | tax_id=85432 13 | Colour= 14 | library_selection_SRX066544=cDNA 15 | library_sample_SRX066544=SRS211150 16 | sample_longLabel_SRS211150= 17 | sample_shortLabel_SRS211150= 18 | sample_ChEBI_ID_SRS211150= 19 | sample_WormBaseLifeStage_SRS211150= 20 | 21 | [GENERAL] 22 | general_bioproject= 23 | -------------------------------------------------------------------------------- /config/worm/Aphelenchoides_besseyi.ini: -------------------------------------------------------------------------------- 1 | [SRP033379] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Aphelenchoides besseyi 8 | secondary_study_accession=SRP033379 9 | study_accession=PRJNA229675 10 | study_title=Aphelenchoides besseyi Transcriptome or Gene expression 11 | center_name=Northeast Forestry University 12 | tax_id=269767 13 | Colour= 14 | study_description=Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed stage population of A. besseyi. 15 | library_selection_SRX385206=other 16 | library_sample_SRX385206=SRS509362 17 | sample_longLabel_SRS509362= 18 | sample_shortLabel_SRS509362= 19 | sample_ChEBI_ID_SRS509362= 20 | sample_WormBaseLifeStage_SRS509362= 21 | -------------------------------------------------------------------------------- /config/worm/Bdellocephala_annandalei.ini: -------------------------------------------------------------------------------- 1 | [DRP001311] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Bdellocephala annandalei 8 | secondary_study_accession=DRP001311 9 | study_accession=PRJDB1529 10 | study_title=Transcriptome analysis of Bdellocephala annandalei 11 | center_name=NAGAHAMA_BIO 12 | tax_id=1421413 13 | Colour= 14 | study_description=To find out the change of gene expression of B. annandalei under low-oxygen conditions 15 | library_selection_DRX013308=unspecified 16 | library_sample_DRX013308=DRS013071 17 | sample_longLabel_DRS013071= 18 | sample_shortLabel_DRS013071= 19 | sample_ChEBI_ID_DRS013071= 20 | sample_WormBaseLifeStage_DRS013071= 21 | -------------------------------------------------------------------------------- /config/worm/Bdelloura_candida.ini: -------------------------------------------------------------------------------- 1 | [SRP057226] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Bdelloura candida 8 | secondary_study_accession=SRP057226 9 | study_accession=PRJNA277606 10 | study_title=Bdelloura candida Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=46766 13 | Colour= 14 | study_description=This is a cDNA library prepared from a single individual using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX997151=PolyA 16 | library_sample_SRX997151=SRS911385 17 | sample_longLabel_SRS911385= 18 | sample_shortLabel_SRS911385= 19 | sample_ChEBI_ID_SRS911385= 20 | sample_WormBaseLifeStage_SRS911385= 21 | -------------------------------------------------------------------------------- /config/worm/Bothriomolus_balticus.ini: -------------------------------------------------------------------------------- 1 | [SRP057030] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Bothriomolus balticus 8 | secondary_study_accession=SRP057030 9 | study_accession=PRJNA277605 10 | study_title=Bothriomolus balticus Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628682 13 | Colour= 14 | study_description=This is a cDNA library prepared from multiple adults pooled prior to RNA-extraction, and amplified using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX980534=PolyA 16 | library_sample_SRX980534=SRS900406 17 | sample_longLabel_SRS900406= 18 | sample_shortLabel_SRS900406= 19 | sample_ChEBI_ID_SRS900406= 20 | sample_WormBaseLifeStage_SRS900406= 21 | -------------------------------------------------------------------------------- /config/worm/Bursaphelenchus_mucronatus.ini: -------------------------------------------------------------------------------- 1 | [SRP008063] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Bursaphelenchus mucronatus 8 | secondary_study_accession=SRP008063 9 | study_accession=SRP008063 10 | study_title=Comparative Transcriptomes Analysis of Two Pinewood Nematodes Bursaphelenchus xylophilus and Bursaphelenchus mucronatus by Deep-Sequencing Technology 11 | center_name=Individual 12 | tax_id=6325 13 | Colour= 14 | library_selection_SRX096027=RANDOM 15 | library_sample_SRX096027=SRS259967 16 | sample_longLabel_SRS259967= 17 | sample_shortLabel_SRS259967= 18 | sample_ChEBI_ID_SRS259967= 19 | sample_WormBaseLifeStage_SRS259967= 20 | -------------------------------------------------------------------------------- /config/worm/Caenorhabditis_angaria.ini: -------------------------------------------------------------------------------- 1 | [SRP003492] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Caenorhabditis angaria 8 | secondary_study_accession=SRP003492 9 | study_accession=PRJNA51225 10 | study_title=Caenorhabditis angaria genome sequencing project 11 | center_name=Cal. Inst. of Tech., Division of Biology 12 | tax_id=860376 13 | Colour= 14 | study_description=This strain will be used for comparative genome analysis. 15 | library_selection_SRX026727=cDNA 16 | library_sample_SRX026727=SRS114803 17 | sample_longLabel_SRS114803= 18 | sample_shortLabel_SRS114803= 19 | sample_ChEBI_ID_SRS114803= 20 | sample_WormBaseLifeStage_SRS114803= 21 | -------------------------------------------------------------------------------- /config/worm/Catenula_lemnae.ini: -------------------------------------------------------------------------------- 1 | [SRP053430] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Catenula lemnae 8 | secondary_study_accession=SRP053430 9 | study_accession=PRJNA274961 10 | study_title=Catenula lemnae Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=570249 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Catenula lemnae 15 | library_selection_SRX871445=unspecified 16 | library_sample_SRX871445=SRS842088 17 | sample_longLabel_SRS842088= 18 | sample_shortLabel_SRS842088= 19 | sample_ChEBI_ID_SRS842088= 20 | sample_WormBaseLifeStage_SRS842088= 21 | -------------------------------------------------------------------------------- /config/worm/Dictyocaulus_filaria.ini: -------------------------------------------------------------------------------- 1 | [SRP032224] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Dictyocaulus filaria 8 | secondary_study_accession=SRP032224 9 | study_accession=PRJNA222411 10 | study_title=Dictyocaulus filariaTranscriptome or Gene expression 11 | center_name=Melbourne University 12 | tax_id=44603 13 | Colour= 14 | study_description=We established and used a bioinformatic workflow to compare, both qualitatively and quantitatively, the transcriptomes of the adult stages of the lungworms Dictyocaulus filaria and D. viviparus in the absence of reference genomes. 15 | library_selection_SRX368686=unspecified 16 | library_sample_SRX368686=SRS494410 17 | sample_longLabel_SRS494410= 18 | sample_shortLabel_SRS494410= 19 | sample_ChEBI_ID_SRS494410= 20 | sample_WormBaseLifeStage_SRS494410= 21 | -------------------------------------------------------------------------------- /config/worm/Echinoplana_celerrima.ini: -------------------------------------------------------------------------------- 1 | [SRP053432] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Echinoplana celerrima 8 | secondary_study_accession=SRP053432 9 | study_accession=PRJNA274964 10 | study_title=Echinoplana celerrima Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=983673 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Echinoplana celerrima 15 | library_selection_SRX871508=unspecified 16 | library_sample_SRX871508=SRS842092 17 | sample_longLabel_SRS842092= 18 | sample_shortLabel_SRS842092= 19 | sample_ChEBI_ID_SRS842092= 20 | sample_WormBaseLifeStage_SRS842092= 21 | -------------------------------------------------------------------------------- /config/worm/Enoplus_brevis.ini: -------------------------------------------------------------------------------- 1 | [ERP008507] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Enoplus brevis 8 | secondary_study_accession=ERP008507 9 | study_accession=PRJEB7588 10 | study_title=The genome and transcriptome of the marine nematode Enoplus brevis. 11 | center_name=BANG 12 | tax_id=57292 13 | Colour= 14 | study_description=The genome and transcriptome of the marine nematode Enoplus brevis. 15 | library_selection_ERX616982=RANDOM 16 | library_sample_ERX616982=ERS571105 17 | sample_longLabel_ERS571105= 18 | sample_shortLabel_ERS571105= 19 | sample_ChEBI_ID_ERS571105= 20 | sample_WormBaseLifeStage_ERS571105= 21 | -------------------------------------------------------------------------------- /config/worm/Fascioloides_magna.ini: -------------------------------------------------------------------------------- 1 | [SRP013117] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Fascioloides magna 8 | secondary_study_accession=SRP013117 9 | study_accession=SRP013117 10 | study_title=A deep exploration of the transcriptome and ‘excretory/secretory’ proteome of adult Fascioloides magna 11 | center_name=The University of Melbourne 12 | tax_id=394415 13 | Colour= 14 | library_selection_SRX147910=RANDOM 15 | library_sample_SRX147910=SRS333832 16 | sample_longLabel_SRS333832= 17 | sample_shortLabel_SRS333832= 18 | sample_ChEBI_ID_SRS333832= 19 | sample_WormBaseLifeStage_SRS333832= 20 | -------------------------------------------------------------------------------- /config/worm/Geocentrophora_applanata.ini: -------------------------------------------------------------------------------- 1 | [SRP056919] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Geocentrophora applanata 8 | secondary_study_accession=SRP056919 9 | study_accession=PRJNA277633 10 | study_title=Geocentrophora applanata Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1468192 13 | Colour= 14 | study_description=This is a cDNA constructed from multiple starved adults and embryos pooled prior to RNA extraction, using the Illumina TruSeq RNA v2 protocol, and sequenced in multiplex 2x100bp on an Illumina HiSeq 2000. Further specimen information is available at MCZbase under accession IZ26504. 15 | library_selection_SRX981000=PolyA 16 | library_sample_SRX981000=SRS895859 17 | sample_longLabel_SRS895859= 18 | sample_shortLabel_SRS895859= 19 | sample_ChEBI_ID_SRS895859= 20 | sample_WormBaseLifeStage_SRS895859= 21 | -------------------------------------------------------------------------------- /config/worm/Geocentrophora_sphyrocephala.ini: -------------------------------------------------------------------------------- 1 | [SRP053435] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Geocentrophora sphyrocephala 8 | secondary_study_accession=SRP053435 9 | study_accession=PRJNA275047 10 | study_title=Geocentrophora sphyrocephala Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=6176 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Geocentrophora sphyrocephala 15 | library_selection_SRX871533=unspecified 16 | library_sample_SRX871533=SRS842123 17 | sample_longLabel_SRS842123= 18 | sample_shortLabel_SRS842123= 19 | sample_ChEBI_ID_SRS842123= 20 | sample_WormBaseLifeStage_SRS842123= 21 | -------------------------------------------------------------------------------- /config/worm/Girardia.ini: -------------------------------------------------------------------------------- 1 | [SRP070966] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Girardia 8 | secondary_study_accession=SRP070966 9 | study_accession=PRJNA313460 10 | study_title=Girardia sp Transcriptome or Gene expression 11 | center_name=SUB1364667 12 | tax_id=52316 13 | Colour= 14 | study_description=Giardia sp. Transcriptome 15 | library_selection_SRX1605771=unspecified 16 | library_sample_SRX1605771=SRS1315406 17 | sample_longLabel_SRS1315406= 18 | sample_shortLabel_SRS1315406= 19 | sample_ChEBI_ID_SRS1315406= 20 | sample_WormBaseLifeStage_SRS1315406= 21 | -------------------------------------------------------------------------------- /config/worm/Halomonhystera_disjuncta.ini: -------------------------------------------------------------------------------- 1 | [SRP050898] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Halomonhystera disjuncta 8 | secondary_study_accession=SRP050898 9 | study_accession=PRJNA268901 10 | study_title=Halomonhystera Transcriptome or Gene expression 11 | center_name=Ghent University 12 | tax_id=535939 13 | Colour= 14 | study_description=Comparison of the transcriptome of a intertidal and deep-sea nematode to elucidate the adaptation and evolutionary to difference in relation to the environment 15 | library_selection_SRX764337=PolyA 16 | library_sample_SRX764337=SRS748703 17 | sample_longLabel_SRS748703= 18 | sample_shortLabel_SRS748703= 19 | sample_ChEBI_ID_SRS748703= 20 | sample_WormBaseLifeStage_SRS748703= 21 | -------------------------------------------------------------------------------- /config/worm/Halomonhystera_hermesi.ini: -------------------------------------------------------------------------------- 1 | [SRP050898] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Halomonhystera hermesi 8 | secondary_study_accession=SRP050898 9 | study_accession=PRJNA268901 10 | study_title=Halomonhystera Transcriptome or Gene expression 11 | center_name=Ghent University 12 | tax_id=1573192 13 | Colour= 14 | study_description=Comparison of the transcriptome of a intertidal and deep-sea nematode to elucidate the adaptation and evolutionary to difference in relation to the environment 15 | library_selection_SRX764336=PolyA 16 | library_sample_SRX764336=SRS748702 17 | sample_longLabel_SRS748702= 18 | sample_shortLabel_SRS748702= 19 | sample_ChEBI_ID_SRS748702= 20 | sample_WormBaseLifeStage_SRS748702= 21 | -------------------------------------------------------------------------------- /config/worm/Heterodera_glycines.ini: -------------------------------------------------------------------------------- 1 | [SRP070586] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Heterodera glycines 8 | secondary_study_accession=SRP070586 9 | study_accession=PRJNA312063 10 | study_title=Parasitic Nematode Glands Gene expression 11 | center_name=WUGSC 12 | tax_id=51029 13 | Colour= 14 | study_description=This project will study the genes expressed in gland cells in nematodes. 15 | library_selection_SRX1600830=unspecified 16 | library_sample_SRX1600830=SRS1310707 17 | sample_longLabel_SRS1310707= 18 | sample_shortLabel_SRS1310707= 19 | sample_ChEBI_ID_SRS1310707= 20 | sample_WormBaseLifeStage_SRS1310707= 21 | -------------------------------------------------------------------------------- /config/worm/Hirschmanniella_oryzae.ini: -------------------------------------------------------------------------------- 1 | [SRP009636] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Hirschmanniella oryzae 8 | secondary_study_accession=SRP009636 9 | study_accession=SRP009636 10 | study_title=Analysis of the transcriptome of Hirschmanniella oryzae 11 | center_name=Ghent University 12 | tax_id=362338 13 | Colour= 14 | library_selection_SRX110506=unspecified 15 | library_sample_SRX110506=SRS281726 16 | sample_longLabel_SRS281726= 17 | sample_shortLabel_SRS281726= 18 | sample_ChEBI_ID_SRS281726= 19 | sample_WormBaseLifeStage_SRS281726= 20 | -------------------------------------------------------------------------------- /config/worm/Itaspiella_helgolandica.ini: -------------------------------------------------------------------------------- 1 | [SRP053637] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Itaspiella helgolandica 8 | secondary_study_accession=SRP053637 9 | study_accession=PRJNA275050 10 | study_title=Itaspiella helgolandica Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1611829 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Itaspiella helgolandica 15 | library_selection_SRX872314=unspecified 16 | library_sample_SRX872314=SRS842635 17 | sample_longLabel_SRS842635= 18 | sample_shortLabel_SRS842635= 19 | sample_ChEBI_ID_SRS842635= 20 | sample_WormBaseLifeStage_SRS842635= 21 | -------------------------------------------------------------------------------- /config/worm/Lehardyia_sp._CEL-2015.ini: -------------------------------------------------------------------------------- 1 | [SRP057525] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Lehardyia sp. CEL-2015 8 | secondary_study_accession=SRP057525 9 | study_accession=PRJNA277603 10 | study_title=Lehardyia sp. CEL-2015 Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628667 13 | Colour= 14 | study_description=This is a cDNA library prepared from a single individual using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX997426=PolyA 16 | library_sample_SRX997426=SRS916819 17 | sample_longLabel_SRS916819= 18 | sample_shortLabel_SRS916819= 19 | sample_ChEBI_ID_SRS916819= 20 | sample_WormBaseLifeStage_SRS916819= 21 | -------------------------------------------------------------------------------- /config/worm/Leptoplana_tremellaris.ini: -------------------------------------------------------------------------------- 1 | [SRP053639] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Leptoplana tremellaris 8 | secondary_study_accession=SRP053639 9 | study_accession=PRJNA275053 10 | study_title=Leptoplana tremellaris Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=107733 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Leptoplana tremellaris 15 | library_selection_SRX872321=unspecified 16 | library_sample_SRX872321=SRS842637 17 | sample_longLabel_SRS842637= 18 | sample_shortLabel_SRS842637= 19 | sample_ChEBI_ID_SRS842637= 20 | sample_WormBaseLifeStage_SRS842637= 21 | -------------------------------------------------------------------------------- /config/worm/Loa_loa.ini: -------------------------------------------------------------------------------- 1 | [SRP011638] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Loa loa 8 | secondary_study_accession=SRP011638 9 | study_accession=PRJNA60555 10 | study_title=Loa loa transcriptome sequencing project 11 | center_name=BI 12 | tax_id=7209 13 | Colour= 14 | study_description=RNA was provided by Doran Fink and Thomas Nutman at NIH. Loa Loa is a filarial worm and causative agent of filariasis in humans. 15 | library_selection_SRX130438=cDNA 16 | library_sample_SRX130438=SRS301861 17 | sample_longLabel_SRS301861= 18 | sample_shortLabel_SRS301861= 19 | sample_ChEBI_ID_SRS301861= 20 | sample_WormBaseLifeStage_SRS301861= 21 | -------------------------------------------------------------------------------- /config/worm/Longidorus_elongatus.ini: -------------------------------------------------------------------------------- 1 | [ERP009400] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Longidorus elongatus 8 | secondary_study_accession=ERP009400 9 | study_accession=PRJEB8328 10 | study_title=Longidorus elongatus mixed stage RNAseq 11 | center_name=James Hutton Institute 12 | tax_id=70231 13 | Colour= 14 | study_description=A single lane of Illumina MiSeq was used to sequence a cDNA library prepared from mixed stage Longidorus elongatus with 150 base pair paired end reads. 15 | library_selection_ERX688304=RT-PCR 16 | library_sample_ERX688304=ERS647085 17 | sample_longLabel_ERS647085= 18 | sample_shortLabel_ERS647085= 19 | sample_ChEBI_ID_ERS647085= 20 | sample_WormBaseLifeStage_ERS647085= 21 | -------------------------------------------------------------------------------- /config/worm/Maritigrella_crozieri.ini: -------------------------------------------------------------------------------- 1 | [SRP054950] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Maritigrella crozieri 8 | secondary_study_accession=SRP054950 9 | study_accession=PRJNA275060 10 | study_title=Maritigrella crozieri Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=526434 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Maritigrella crozieri 15 | library_selection_SRX875739=unspecified 16 | library_sample_SRX875739=SRS844631 17 | library_selection_SRX875742=unspecified 18 | library_sample_SRX875742=SRS844631 19 | sample_longLabel_SRS844631= 20 | sample_shortLabel_SRS844631= 21 | sample_ChEBI_ID_SRS844631= 22 | sample_WormBaseLifeStage_SRS844631= 23 | -------------------------------------------------------------------------------- /config/worm/Meloidogyne_graminicola.ini: -------------------------------------------------------------------------------- 1 | [SRP014208] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Meloidogyne graminicola 8 | secondary_study_accession=SRP014208 9 | study_accession=PRJNA170484 10 | study_title=Meloidogyne graminicolaTranscriptome or Gene expression 11 | center_name=Ghent University 12 | tax_id=189291 13 | Colour= 14 | study_description=The goal of this project is to generate transcriptome data from preparasitic juveniles of Meloidogyne graminicola. This data can subsequently be used for the identification of effector genes, i.e. genes that play a role in the parasitic interaction with rice. 15 | library_selection_SRX159200=RANDOM 16 | library_sample_SRX159200=SRS349675 17 | sample_longLabel_SRS349675= 18 | sample_shortLabel_SRS349675= 19 | sample_ChEBI_ID_SRS349675= 20 | sample_WormBaseLifeStage_SRS349675= 21 | -------------------------------------------------------------------------------- /config/worm/Mesostoma_lingua.ini: -------------------------------------------------------------------------------- 1 | [SRP053647] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Mesostoma lingua 8 | secondary_study_accession=SRP053647 9 | study_accession=PRJNA275061 10 | study_title=Mesostoma lingua Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=99405 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Mesostoma lingua 15 | library_selection_SRX872347=unspecified 16 | library_sample_SRX872347=SRS842663 17 | sample_longLabel_SRS842663= 18 | sample_shortLabel_SRS842663= 19 | sample_ChEBI_ID_SRS842663= 20 | sample_WormBaseLifeStage_SRS842663= 21 | -------------------------------------------------------------------------------- /config/worm/Microdalyellia_fusca.ini: -------------------------------------------------------------------------------- 1 | [SRP053651] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Microdalyellia fusca 8 | secondary_study_accession=SRP053651 9 | study_accession=PRJNA275064 10 | study_title=Microdalyellia fusca Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1311901 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Microdalyellia fusca 15 | library_selection_SRX872356=unspecified 16 | library_sample_SRX872356=SRS842668 17 | sample_longLabel_SRS842668= 18 | sample_shortLabel_SRS842668= 19 | sample_ChEBI_ID_SRS842668= 20 | sample_WormBaseLifeStage_SRS842668= 21 | -------------------------------------------------------------------------------- /config/worm/Microdalyellia_schmidti.ini: -------------------------------------------------------------------------------- 1 | [SRP053655] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Microdalyellia schmidti 8 | secondary_study_accession=SRP053655 9 | study_accession=PRJNA275065 10 | study_title=Microdalyellia schmidti Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1611830 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Microdalyellia schmidti 15 | library_selection_SRX872362=unspecified 16 | library_sample_SRX872362=SRS842672 17 | sample_longLabel_SRS842672= 18 | sample_shortLabel_SRS842672= 19 | sample_ChEBI_ID_SRS842672= 20 | sample_WormBaseLifeStage_SRS842672= 21 | -------------------------------------------------------------------------------- /config/worm/Microdalyellia_sp._CEL-2015.ini: -------------------------------------------------------------------------------- 1 | [SRP057447] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Microdalyellia sp. CEL-2015 8 | secondary_study_accession=SRP057447 9 | study_accession=PRJNA277602 10 | study_title=Microdalyellia sp. CEL-2015 Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628671 13 | Colour= 14 | study_description=This is a cDNA library prepared from a single individual using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX998816=PolyA 16 | library_sample_SRX998816=SRS914130 17 | sample_longLabel_SRS914130= 18 | sample_shortLabel_SRS914130= 19 | sample_ChEBI_ID_SRS914130= 20 | sample_WormBaseLifeStage_SRS914130= 21 | -------------------------------------------------------------------------------- /config/worm/Monocelis_fusca.ini: -------------------------------------------------------------------------------- 1 | [SRP057383] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Monocelis fusca 8 | secondary_study_accession=SRP057383 9 | study_accession=PRJNA277600 10 | study_title=Monocelis fusca Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=983168 13 | Colour= 14 | study_description=This is a cDNA library prepared from several dozen adults at various stages of development, pooled prior to RNA extraction, prepared using the Illumina TruSeq RNA v2 protocol, and sequenced in multiplex 2x100 bp on an Illumina HiSeq 2000. More specimen data can be found at MCZbase under accession IZ26672. 15 | library_selection_SRX998836=PolyA 16 | library_sample_SRX998836=SRS912980 17 | sample_longLabel_SRS912980= 18 | sample_shortLabel_SRS912980= 19 | sample_ChEBI_ID_SRS912980= 20 | sample_WormBaseLifeStage_SRS912980= 21 | -------------------------------------------------------------------------------- /config/worm/Monocelis_sp._BE-2015.ini: -------------------------------------------------------------------------------- 1 | [SRP055136] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Monocelis sp. BE-2015 8 | secondary_study_accession=SRP055136 9 | study_accession=PRJNA275067 10 | study_title=Monocelis sp. BE-2015 Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1597771 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Monocelis sp. 15 | library_selection_SRX883021=unspecified 16 | library_sample_SRX883021=SRS850388 17 | sample_longLabel_SRS850388= 18 | sample_shortLabel_SRS850388= 19 | sample_ChEBI_ID_SRS850388= 20 | sample_WormBaseLifeStage_SRS850388= 21 | -------------------------------------------------------------------------------- /config/worm/Opisthorchis_viverrini.ini: -------------------------------------------------------------------------------- 1 | [SRP013211] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Opisthorchis viverrini 8 | secondary_study_accession=SRP013211 9 | study_accession=SRP013211 10 | study_title=Molecular changes in Opisthorchis viverrini (Southeast Asian liver fluke) during the transition from the juvenile to adult stage 11 | center_name=The University of Melbourne 12 | tax_id=6198 13 | Colour= 14 | library_selection_SRX148330=RANDOM 15 | library_sample_SRX148330=SRS334085 16 | library_selection_SRX148331=RANDOM 17 | library_sample_SRX148331=SRS334086 18 | sample_longLabel_SRS334086= 19 | sample_shortLabel_SRS334086= 20 | sample_ChEBI_ID_SRS334086= 21 | sample_WormBaseLifeStage_SRS334086= 22 | sample_longLabel_SRS334085= 23 | sample_shortLabel_SRS334085= 24 | sample_ChEBI_ID_SRS334085= 25 | sample_WormBaseLifeStage_SRS334085= 26 | -------------------------------------------------------------------------------- /config/worm/Panagrolaimus_davidi.ini: -------------------------------------------------------------------------------- 1 | [SRP041973] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Panagrolaimus davidi 8 | secondary_study_accession=SRP041973 9 | study_accession=PRJNA247454 10 | study_title=Panagrolaimus davidi strain:CB1 Transcriptome or Gene expression 11 | center_name=British Antarctic Survey 12 | tax_id=227884 13 | Colour= 14 | study_description=RNA-seq for sequencing and assembling the transcriptome of Panagrolaimus davidi 15 | library_selection_SRX542217=PCR 16 | library_sample_SRX542217=SRS606665 17 | sample_longLabel_SRS606665= 18 | sample_shortLabel_SRS606665= 19 | sample_ChEBI_ID_SRS606665= 20 | sample_WormBaseLifeStage_SRS606665= 21 | -------------------------------------------------------------------------------- /config/worm/Paragonimus_skrjabini.ini: -------------------------------------------------------------------------------- 1 | [SRP067887] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Paragonimus skrjabini 8 | secondary_study_accession=SRP067887 9 | study_accession=PRJNA301597 10 | study_title=Paragonimus skrjabini Transcriptome or Gene expression 11 | center_name=WUGSC 12 | tax_id=59630 13 | Colour= 14 | study_description=The human lung fluke Paragonimus skrjabini represents one of the food-borne helminths infecting humans. These flukes cause paragonimiasis in people and other crab-eating mammals primarily in Asia. 15 | library_selection_SRX1507709=unspecified 16 | library_sample_SRX1507709=SRS1228562 17 | sample_longLabel_SRS1228562= 18 | sample_shortLabel_SRS1228562= 19 | sample_ChEBI_ID_SRS1228562= 20 | sample_WormBaseLifeStage_SRS1228562= 21 | -------------------------------------------------------------------------------- /config/worm/Paragonimus_westermani.ini: -------------------------------------------------------------------------------- 1 | [SRP041509] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Paragonimus westermani 8 | secondary_study_accession=SRP041509 9 | study_accession=PRJNA219632 10 | study_title=Paragonimus westermaniGenome sequencing 11 | center_name=WUGSC 12 | tax_id=34504 13 | Colour= 14 | study_description=Paragonimus spp., lung flukes, represent one of the most injurious of the food-borne helminths. P. westermani is the most common of the food-borne helminths that infect humans. These flukes cause paragonimiasis in people and other crab-eating mammals in Asia, parts of West Africa, and South and Central America 15 | library_selection_SRX1507710=unspecified 16 | library_sample_SRX1507710=SRS1228563 17 | sample_longLabel_SRS1228563= 18 | sample_shortLabel_SRS1228563= 19 | sample_ChEBI_ID_SRS1228563= 20 | sample_WormBaseLifeStage_SRS1228563= 21 | -------------------------------------------------------------------------------- /config/worm/Phagocata_gracilis.ini: -------------------------------------------------------------------------------- 1 | [SRP070949] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Phagocata gracilis 8 | secondary_study_accession=SRP070949 9 | study_accession=PRJNA312785 10 | study_title=Phagocata gracilis Transcriptome or Gene expression 11 | center_name=SUB1353050 12 | tax_id=1354672 13 | Colour= 14 | study_description=Phagocata gracilis Transcriptome 15 | library_selection_SRX1605188=unspecified 16 | library_sample_SRX1605188=SRS1314900 17 | sample_longLabel_SRS1314900= 18 | sample_shortLabel_SRS1314900= 19 | sample_ChEBI_ID_SRS1314900= 20 | sample_WormBaseLifeStage_SRS1314900= 21 | -------------------------------------------------------------------------------- /config/worm/Pratylenchus_coffeae.ini: -------------------------------------------------------------------------------- 1 | [SRP005186] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Pratylenchus coffeae 8 | secondary_study_accession=SRP005186 9 | study_accession=PRJNA79895 10 | study_title=Transcriptome analysis of the lesion nematode Pratylenchus coffeae by 454 sequencing technology 11 | center_name=Ghent University 12 | tax_id=45937 13 | Colour= 14 | study_description=To improve our knowledge on migratory plant-parasitic nematodes, we studied the transcriptome of the nematode Pratylenchus coffeae by generating expressed sequence tags (ESTs). Using the Roche 454 sequencing platform, over 325000 reads were generated. 15 | library_selection_SRX037494=unspecified 16 | library_sample_SRX037494=SRS151337 17 | sample_longLabel_SRS151337= 18 | sample_shortLabel_SRS151337= 19 | sample_ChEBI_ID_SRS151337= 20 | sample_WormBaseLifeStage_SRS151337= 21 | -------------------------------------------------------------------------------- /config/worm/Pratylenchus_penetrans.ini: -------------------------------------------------------------------------------- 1 | [SRP066773] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Pratylenchus penetrans 8 | secondary_study_accession=SRP066773 9 | study_accession=PRJNA304159 10 | study_title=Pratylenchus penetrans transcriptome 11 | center_name=ARS-USDA 12 | tax_id=45929 13 | Colour= 14 | study_description=Pratylenchus penetrans is a plan-parasitic nematode infecting a wide number of host plants 15 | library_selection_SRX1453685=PolyA 16 | library_sample_SRX1453685=SRS1181350 17 | library_selection_SRX1453819=PolyA 18 | library_sample_SRX1453819=SRS1181350 19 | library_selection_SRX1453907=PolyA 20 | library_sample_SRX1453907=SRS1181350 21 | sample_longLabel_SRS1181350= 22 | sample_shortLabel_SRS1181350= 23 | sample_ChEBI_ID_SRS1181350= 24 | sample_WormBaseLifeStage_SRS1181350= 25 | -------------------------------------------------------------------------------- /config/worm/Prionchulus_punctatus.ini: -------------------------------------------------------------------------------- 1 | [ERP008503] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prionchulus punctatus 8 | secondary_study_accession=ERP008503 9 | study_accession=PRJEB7585 10 | study_title=The transcriptome of Prionchulus punctatus 11 | center_name=BANG 12 | tax_id=293874 13 | Colour= 14 | study_description=The transcriptome of Prionchulus punctatus 15 | library_selection_ERX616947=RANDOM 16 | library_sample_ERX616947=ERS570998 17 | library_selection_ERX616948=RANDOM 18 | library_sample_ERX616948=ERS570998 19 | sample_longLabel_ERS570998= 20 | sample_shortLabel_ERS570998= 21 | sample_ChEBI_ID_ERS570998= 22 | sample_WormBaseLifeStage_ERS570998= 23 | -------------------------------------------------------------------------------- /config/worm/Prorhynchus_alpinus.ini: -------------------------------------------------------------------------------- 1 | [SRP057393] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prorhynchus alpinus 8 | secondary_study_accession=SRP057393 9 | study_accession=PRJNA277599 10 | study_title=Prorhynchus alpinus Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1468198 13 | Colour= 14 | study_description=This is a stranded cDNA library prepared from a single individual using the PrepX mRNA protocol on an Apollo324 (IntegenX, now WaferGen), and sequenced in multiplex on an Illumina HiSeq 2000. Further specimen information is available at MCZbase under accession number IZ26514. 15 | library_selection_SRX999312=PolyA 16 | library_sample_SRX999312=SRS913424 17 | sample_longLabel_SRS913424= 18 | sample_shortLabel_SRS913424= 19 | sample_ChEBI_ID_SRS913424= 20 | sample_WormBaseLifeStage_SRS913424= 21 | -------------------------------------------------------------------------------- /config/worm/Prosogynopora_riseri.ini: -------------------------------------------------------------------------------- 1 | [SRP057523] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prosogynopora riseri 8 | secondary_study_accession=SRP057523 9 | study_accession=PRJNA277597 10 | study_title=Prosogynopora riseri Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628673 13 | Colour= 14 | study_description=This is a cDNA library prepared from a single individual using a phi29-mRNA amplification protocol, sequenced in multiplex 2x250 bp on an Illumina MiSeq. More specimen information is available at MCZbase under accession IZXXXXX. 15 | library_selection_SRX998821=PolyA 16 | library_sample_SRX998821=SRS916817 17 | sample_longLabel_SRS916817= 18 | sample_shortLabel_SRS916817= 19 | sample_ChEBI_ID_SRS916817= 20 | sample_WormBaseLifeStage_SRS916817= 21 | -------------------------------------------------------------------------------- /config/worm/Prostheceraeus_vittatus.ini: -------------------------------------------------------------------------------- 1 | [SRP057407] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prostheceraeus vittatus 8 | secondary_study_accession=SRP057407 9 | study_accession=PRJNA277637 10 | study_title=Prostheceraeus vittatus Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=107736 13 | Colour= 14 | study_description=This is a cDNA library that was constructed using adult and embryological material pooled prior to RNA extraction, using the Illumina TruSeq v2 RNA protocol, and sequenced on a full lane of an Illumina HiSeq 2000. 15 | library_selection_SRX999630=PolyA 16 | library_sample_SRX999630=SRS913668 17 | sample_longLabel_SRS913668= 18 | sample_shortLabel_SRS913668= 19 | sample_ChEBI_ID_SRS913668= 20 | sample_WormBaseLifeStage_SRS913668= 21 | -------------------------------------------------------------------------------- /config/worm/Prosthiostomum_siphunculus.ini: -------------------------------------------------------------------------------- 1 | [SRP053679] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Prosthiostomum siphunculus 8 | secondary_study_accession=SRP053679 9 | study_accession=PRJNA275073 10 | study_title=Prosthiostomum siphunculus Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=983679 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Prosthiostomum siphunculus 15 | library_selection_SRX872403=unspecified 16 | library_sample_SRX872403=SRS842699 17 | sample_longLabel_SRS842699= 18 | sample_shortLabel_SRS842699= 19 | sample_ChEBI_ID_SRS842699= 20 | sample_WormBaseLifeStage_SRS842699= 21 | -------------------------------------------------------------------------------- /config/worm/Protomonotresidae_sp._CEL-2015.ini: -------------------------------------------------------------------------------- 1 | [SRP057390] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Protomonotresidae sp. CEL-2015 8 | secondary_study_accession=SRP057390 9 | study_accession=PRJNA277596 10 | study_title=Protomonotresidae sp. CEL-2015 Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628674 13 | Colour= 14 | study_description=This is a stranded cDNA library prepared from a single individual on an Apollo324 machine using the IntegenX (now WaferGen) PrepX mRNA protocol, sequenced in multiplex on an Illumina HiSeq 2000. More specimen information is available at MCZbase under accession IZ27128. 15 | library_selection_SRX999202=PolyA 16 | library_sample_SRX999202=SRS913317 17 | sample_longLabel_SRS913317= 18 | sample_shortLabel_SRS913317= 19 | sample_ChEBI_ID_SRS913317= 20 | sample_WormBaseLifeStage_SRS913317= 21 | -------------------------------------------------------------------------------- /config/worm/Rhynchomesostoma_rostratum.ini: -------------------------------------------------------------------------------- 1 | [SRP057392] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Rhynchomesostoma rostratum 8 | secondary_study_accession=SRP057392 9 | study_accession=PRJNA277594 10 | study_title=Rhynchomesostoma rostratum Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1311950 13 | Colour= 14 | study_description=This is a stranded cDNA library prepared from two adults pooled prior to RNA extraction, using the Apollo324 (IntegenX, now WaferGen) PrepX mRNA protocol, and sequenced in multiplex 2x100 bp on an Illumina HiSeq 2000. 15 | library_selection_SRX999311=PolyA 16 | library_sample_SRX999311=SRS913342 17 | sample_longLabel_SRS913342= 18 | sample_shortLabel_SRS913342= 19 | sample_ChEBI_ID_SRS913342= 20 | sample_WormBaseLifeStage_SRS913342= 21 | -------------------------------------------------------------------------------- /config/worm/Stenostomum_sthenum.ini: -------------------------------------------------------------------------------- 1 | [SRP053680] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Stenostomum sthenum 8 | secondary_study_accession=SRP053680 9 | study_accession=PRJNA275074 10 | study_title=Stenostomum sthenum Transcriptome or Gene expression 11 | center_name=University of Innsbruck 12 | tax_id=1611831 13 | Colour= 14 | study_description=Illumina HiSeq transcriptome of the flatworm Stenostomum sthenum 15 | library_selection_SRX872404=unspecified 16 | library_sample_SRX872404=SRS842700 17 | sample_longLabel_SRS842700= 18 | sample_shortLabel_SRS842700= 19 | sample_ChEBI_ID_SRS842700= 20 | sample_WormBaseLifeStage_SRS842700= 21 | -------------------------------------------------------------------------------- /config/worm/Stylochoplana_maculata.ini: -------------------------------------------------------------------------------- 1 | [SRP041688] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Stylochoplana maculata 8 | secondary_study_accession=SRP041688 9 | study_accession=PRJNA245790 10 | study_title=Phylogenomic studies to elucidate the phylogeny of Spiralia. Transcriptome or Gene expression 11 | center_name=Zoological Research Museum Alexander Koenig 12 | tax_id=1495083 13 | Colour= 14 | study_description=Transcriptomic data of several platyzoan and nemertean species were generated to resolve the relationships of Spiralia with a special emphasis on Platyzoa and to elucidate the origin of Bilateria. 15 | library_selection_SRX534883=cDNA 16 | library_sample_SRX534883=SRS603589 17 | sample_longLabel_SRS603589= 18 | sample_shortLabel_SRS603589= 19 | sample_ChEBI_ID_SRS603589= 20 | sample_WormBaseLifeStage_SRS603589= 21 | -------------------------------------------------------------------------------- /config/worm/Taenia_crassiceps.ini: -------------------------------------------------------------------------------- 1 | [SRP014613] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Taenia crassiceps 8 | secondary_study_accession=SRP014613 9 | study_accession=PRJNA171338 10 | study_title=Taenia crassiceps strain:ORF Transcriptome or Gene expression 11 | center_name=Universidad de Antioquia 12 | tax_id=6207 13 | Colour= 14 | study_description=Transcriptome analysis of the cysticercus stage of the cestode Taenia crassiceps. mRNA was purified and 454 sequenced. 15 | library_selection_SRX171519=RANDOM 16 | library_sample_SRX171519=SRS352306 17 | sample_longLabel_SRS352306= 18 | sample_shortLabel_SRS352306= 19 | sample_ChEBI_ID_SRS352306= 20 | sample_WormBaseLifeStage_SRS352306= 21 | -------------------------------------------------------------------------------- /config/worm/Taenia_pisiformis.ini: -------------------------------------------------------------------------------- 1 | [SRP006907] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Taenia pisiformis 8 | secondary_study_accession=SRP006907 9 | study_accession=SRP006907 10 | study_title=De novo assembly and analysis of high sequencing-based transcriptome data of Taenia pisiformis 11 | center_name=Sichuan Agriculture University 12 | tax_id=85432 13 | Colour= 14 | library_selection_SRX066544=cDNA 15 | library_sample_SRX066544=SRS211150 16 | sample_longLabel_SRS211150= 17 | sample_shortLabel_SRS211150= 18 | sample_ChEBI_ID_SRS211150= 19 | sample_WormBaseLifeStage_SRS211150= 20 | -------------------------------------------------------------------------------- /config/worm/Taenia_saginata.ini: -------------------------------------------------------------------------------- 1 | [SRP046055] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Taenia saginata 8 | secondary_study_accession=SRP046055 9 | study_accession=PRJNA260140 10 | study_title=Taenia saginata Transcriptome or Gene expression 11 | center_name=Lanzhou veterinary research institute, Chinese Aca 12 | tax_id=6206 13 | Colour= 14 | study_description=Analysis of codon usage pattern in Taenia saginata based on a transcriptome dataset 15 | library_selection_SRX691232=PolyA 16 | library_sample_SRX691232=SRS693703 17 | sample_longLabel_SRS693703= 18 | sample_shortLabel_SRS693703= 19 | sample_ChEBI_ID_SRS693703= 20 | sample_WormBaseLifeStage_SRS693703= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_britovi.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella britovi 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=45882 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX986063=unspecified 16 | library_sample_SRX986063=SRS900949 17 | sample_longLabel_SRS900949= 18 | sample_shortLabel_SRS900949= 19 | sample_ChEBI_ID_SRS900949= 20 | sample_WormBaseLifeStage_SRS900949= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_murrelli.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella murrelli 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=144512 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992249=unspecified 16 | library_sample_SRX992249=SRS906996 17 | sample_longLabel_SRS906996= 18 | sample_shortLabel_SRS906996= 19 | sample_ChEBI_ID_SRS906996= 20 | sample_WormBaseLifeStage_SRS906996= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_nativa.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella nativa 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=6335 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX986040=unspecified 16 | library_sample_SRX986040=SRS898754 17 | sample_longLabel_SRS898754= 18 | sample_shortLabel_SRS898754= 19 | sample_ChEBI_ID_SRS898754= 20 | sample_WormBaseLifeStage_SRS898754= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_nelsoni.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella nelsoni 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=6336 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992257=unspecified 16 | library_sample_SRX992257=SRS906999 17 | sample_longLabel_SRS906999= 18 | sample_shortLabel_SRS906999= 19 | sample_ChEBI_ID_SRS906999= 20 | sample_WormBaseLifeStage_SRS906999= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_papuae.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella papuae 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=268474 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX993445=unspecified 16 | library_sample_SRX993445=SRS908054 17 | sample_longLabel_SRS908054= 18 | sample_shortLabel_SRS908054= 19 | sample_ChEBI_ID_SRS908054= 20 | sample_WormBaseLifeStage_SRS908054= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_patagoniensis.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella patagoniensis 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=990121 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992269=unspecified 16 | library_sample_SRX992269=SRS907002 17 | library_selection_SRX992270=unspecified 18 | library_sample_SRX992270=SRS907002 19 | sample_longLabel_SRS907002= 20 | sample_shortLabel_SRS907002= 21 | sample_ChEBI_ID_SRS907002= 22 | sample_WormBaseLifeStage_SRS907002= 23 | -------------------------------------------------------------------------------- /config/worm/Trichinella_sp._T6.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella sp. T6 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=92179 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992253=unspecified 16 | library_sample_SRX992253=SRS906998 17 | sample_longLabel_SRS906998= 18 | sample_shortLabel_SRS906998= 19 | sample_ChEBI_ID_SRS906998= 20 | sample_WormBaseLifeStage_SRS906998= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_sp._T8.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella sp. T8 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=92180 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992261=unspecified 16 | library_sample_SRX992261=SRS907000 17 | sample_longLabel_SRS907000= 18 | sample_shortLabel_SRS907000= 19 | sample_ChEBI_ID_SRS907000= 20 | sample_WormBaseLifeStage_SRS907000= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_sp._T9.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella sp. T9 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=181606 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX992266=unspecified 16 | library_sample_SRX992266=SRS907001 17 | sample_longLabel_SRS907001= 18 | sample_shortLabel_SRS907001= 19 | sample_ChEBI_ID_SRS907001= 20 | sample_WormBaseLifeStage_SRS907001= 21 | -------------------------------------------------------------------------------- /config/worm/Trichinella_zimbabwensis.ini: -------------------------------------------------------------------------------- 1 | [SRP045246] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Trichinella zimbabwensis 8 | secondary_study_accession=SRP045246 9 | study_accession=PRJNA257433 10 | study_title=Annotated genomic assembly for each of the sixteen Trichinella species and genotypes 11 | center_name=University of Melbourne 12 | tax_id=268475 13 | Colour= 14 | study_description=Evolutionary studies of Trichinella species and genotypes. 15 | library_selection_SRX993449=unspecified 16 | library_sample_SRX993449=SRS908055 17 | sample_longLabel_SRS908055= 18 | sample_shortLabel_SRS908055= 19 | sample_ChEBI_ID_SRS908055= 20 | sample_WormBaseLifeStage_SRS908055= 21 | -------------------------------------------------------------------------------- /config/worm/Xenoprorhynchus_sp._I_CEL-2015.ini: -------------------------------------------------------------------------------- 1 | [SRP057520] 2 | use= 3 | remark= 4 | pubmed= 5 | status= 6 | ArrayExpress_ID= 7 | scientific_name=Xenoprorhynchus sp. I CEL-2015 8 | secondary_study_accession=SRP057520 9 | study_accession=PRJNA277588 10 | study_title=Xenoprorhynchus sp. I CEL-2015 Transcriptome or Gene expression 11 | center_name=Harvard University 12 | tax_id=1628678 13 | Colour= 14 | study_description=This is a stranded cDNA library prepared from a single individual on an Apollo324 machine using the IntegenX (now WaferGen) PrepX mRNA protocol, sequenced in multiplex on an Illumina HiSeq 2000. More specimen information is available at MCZbase under accession IZ26513. 15 | library_selection_SRX999217=PolyA 16 | library_sample_SRX999217=SRS916814 17 | sample_longLabel_SRS916814= 18 | sample_shortLabel_SRS916814= 19 | sample_ChEBI_ID_SRS916814= 20 | sample_WormBaseLifeStage_SRS916814= 21 | -------------------------------------------------------------------------------- /cpanfile: -------------------------------------------------------------------------------- 1 | requires 'Ace'; 2 | requires 'Tk::SplitFrame'; # for the curation tools 3 | requires 'Net::FTPSSL'; # for ENA submissions 4 | requires 'DateTime'; # for GO-GAF format > 2.2 5 | -------------------------------------------------------------------------------- /parasite/checks/biomart_taxon_tree.t: -------------------------------------------------------------------------------- 1 | use strict; 2 | use warnings; 3 | use ProductionMysql; 4 | use Test::More; 5 | use LWP::Simple; 6 | use File::Slurp qw/read_file/; 7 | 8 | my ($doc_path) = @ARGV; 9 | $doc_path //= "http://test.parasite.wormbase.org/taxon_tree_data.js"; 10 | my $doc = -f $doc_path ? read_file $doc_path : get $doc_path; 11 | 12 | like($doc, qr/^taxonTreeData =/, "Doc with taxonTreeData"); 13 | 14 | subtest "All species mentioned in the doc" => sub { 15 | ok ($doc =~ /$_/, "Doc has: $_") for ProductionMysql->staging->species; 16 | }; 17 | 18 | subtest "All biomart names mentioned in the doc" => sub { 19 | ok ($doc =~ /$_/, "Doc has: $_") for sort map {ProductionMysql::core_db_to_biomart_name($_) } ProductionMysql->staging->core_databases; 20 | }; 21 | 22 | done_testing; 23 | -------------------------------------------------------------------------------- /parasite/modules/IdMapping/TemporaryIdGenerator.pm: -------------------------------------------------------------------------------- 1 | package IdMapping::TemporaryIdGenerator; 2 | 3 | use strict; 4 | use warnings; 5 | 6 | use base qw(Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric); 7 | 8 | sub increment_stable_id { 9 | my ( $self, $lastId ) = @_; 10 | 11 | $lastId =~ /^Tmp([GTEP])(\d{11})$/ or die "invalid stable ID: $lastId."; 12 | my $num = $2+1; 13 | return sprintf("Tmp%s%011d",$1,$num); 14 | 15 | } 16 | 17 | sub is_valid { 18 | my ( $self, $stableId ) = @_; 19 | 20 | if ( defined($stableId) && $stableId =~ /^Tmp([GTEP])(\d{11})$/) 21 | {return 1} else {return undef} 22 | } 23 | 24 | 1; 25 | -------------------------------------------------------------------------------- /parasite/modules/MysqlPair.pm: -------------------------------------------------------------------------------- 1 | use strict; 2 | use Carp; 3 | use ProductionMysql; 4 | package MysqlPair; 5 | sub new { 6 | my ($class, $from, $to) = @_; 7 | Carp::croak "Usage: MysqlDump->new(\$from, \$to)" unless $from and $to; 8 | $from = ProductionMysql->new($from) unless ref $from eq 'ProductionMysql'; 9 | $to = ProductionMysql->new($to) unless ref $to eq 'ProductionMysql'; 10 | return bless {from => $from, to => $to}, $class; 11 | } 12 | sub dump { 13 | my ($self, $pattern, $table) = @_; 14 | my $core_db_from = $self->{from}->core_db($pattern); 15 | my $core_db_to = $self->{to}->core_db($pattern); 16 | my $from_cmd = $self->{from}->{db_cmd} . " mysqldump $core_db_from $table " ; 17 | my $to_cmd = $self->{to}->{db_cmd} . " $core_db_to " ; 18 | return system ("{ $from_cmd | $to_cmd 2>&1 1>&3 | grep -v insecure 1>&2; } 3>&1 "); 19 | } 20 | 1; 21 | -------------------------------------------------------------------------------- /parasite/modules/PipeConfig/ParaSiteLoadMembers_conf.pm: -------------------------------------------------------------------------------- 1 | package PipeConfig::ParaSiteLoadMembers_conf; 2 | 3 | use strict; 4 | use warnings; 5 | 6 | use base('Bio::EnsEMBL::Compara::PipeConfig::EG::LoadMembers_conf'); 7 | 8 | sub default_options { 9 | my ($self) = @_; 10 | return { 11 | %{$self->SUPER::default_options}, 12 | exclude_gene_analysis => { 'macrostomum_lignano_prjna284736' => ['mlignano_schatz_gene_bad'] }, 13 | curr_core_sources_locs => [], 14 | prev_core_sources_locs => [], 15 | reuse_member_db => 0, 16 | reg_conf => "$ENV{PARASITE_CONF}/compara.registry.pm", 17 | } ; 18 | } 19 | 1; 20 | -------------------------------------------------------------------------------- /parasite/modules/python/Deployment.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | def rsync_to_external_location_command(directory_from, remote_path, method="embassy"): 4 | if method == "embassy": 5 | return(rsync_dir_to_external_location_embassy_bucket_command(directory_from, remote_path)) 6 | else: 7 | exit_with_error("You can only copy files to embassy right now.") 8 | 9 | def rsync_dir_to_external_location_embassy_bucket_command(directory_from, embassy_path): 10 | bash_command = "module load embassy\n\n" + \ 11 | "eaws s3 sync " + directory_from + " " + \ 12 | embassy_path 13 | return bash_command -------------------------------------------------------------------------------- /parasite/scripts/production/.add_orthologs_to_ftp.pl.swp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/parasite/scripts/production/.add_orthologs_to_ftp.pl.swp -------------------------------------------------------------------------------- /parasite/scripts/production/.compare_ftp_dirs.pl.swp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/parasite/scripts/production/.compare_ftp_dirs.pl.swp -------------------------------------------------------------------------------- /parasite/scripts/production/apollo/create_new_apollo_instance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/parasite/scripts/production/apollo/create_new_apollo_instance.py -------------------------------------------------------------------------------- /parasite/scripts/production/apollo/sanger_prepare.sh: -------------------------------------------------------------------------------- 1 | function sanger_prepare { 2 | ssh -f -N -C -X ssh.sanger.ac.uk 3 | ssh -f -N -C -X sangerfarm 4 | } 5 | 6 | function sanger_connect { 7 | sanger_prepare; 8 | ssh sangerngs; 9 | } 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /parasite/scripts/production/core-creation/fasta_parsing_commands.sh: -------------------------------------------------------------------------------- 1 | splitfa(){ 2 | i=1; 3 | cat $1 | while read line ; do 4 | if [ ${line:0:1} == ">" ] ; then 5 | header="$line" 6 | echo "$header" >> seq"${i}".fasta 7 | ((i++)) 8 | else 9 | seq="$line" 10 | echo "$seq" >> seq"${i}".fasta 11 | fi 12 | done 13 | } -------------------------------------------------------------------------------- /parasite/scripts/production/core-creation/healthcheck.pl: -------------------------------------------------------------------------------- 1 | use CoreCreation::Conf; 2 | use File::Spec; 3 | use File::Basename; 4 | 5 | my $conf = CoreCreation::Conf->new(shift) or die "usage: $0 "; 6 | 7 | my $fasta = $conf -> {fasta}; 8 | my $gff3 = $conf -> {gff3}; 9 | my $db_name = $conf -> {core_database}->{dbname}; 10 | my $host = $conf -> {core_database}->{host}; 11 | my $port = $conf -> {core_database}->{port}; 12 | 13 | my $healthcheck_script = File::Spec->catfile(dirname($0) , "healthcheck.sh"); 14 | system("$healthcheck_script -d $db_name -g $fasta -a $gff3 -u ensro -p $port -s $host"); 15 | 16 | -------------------------------------------------------------------------------- /parasite/scripts/production/core-creation/reformat_gff_dependencies.py: -------------------------------------------------------------------------------- 1 | transcript_types = ["mRNA", "tRNA", "rRNA", "transcript","nontranslating_transcript", 2 | "ncRNA", "snRNA", "tRNA_pseudogene", 3 | "snoRNA", "scRNA", "piRNA", "lincRNA", 4 | "asRNA", "miRNA_mature", "miRNA"] 5 | 6 | coding_transcript_types = ["mRNA", "transcript"] 7 | 8 | gene_types = ["gene", "pseudogene"] 9 | 10 | wormbase_source = "WormBase_imported" -------------------------------------------------------------------------------- /parasite/scripts/production/core-creation/remove_scaffolds_from_fasta.py: -------------------------------------------------------------------------------- 1 | from Bio import SeqIO 2 | from ProductionUtils import * 3 | import sys 4 | 5 | scaffolds_tsv = sys.argv[1] 6 | input_fasta = sys.argv[2] 7 | 8 | blacklisted_scaffolds = csvlines2list(scaffolds_tsv) 9 | 10 | ffile = SeqIO.parse(sys.argv[2], "fasta") 11 | header_set = set(line.strip() for line in flatten(blacklisted_scaffolds)) 12 | 13 | for seq_record in ffile: 14 | try: 15 | header_set.remove(seq_record.name) 16 | except KeyError: 17 | print(seq_record.format("fasta")) 18 | continue 19 | if len(header_set) != 0: 20 | print(len(header_set),'of the headers from list were not identified in the input fasta file.', file=sys.stderr) -------------------------------------------------------------------------------- /parasite/scripts/production/create_config_file_for_datachecks.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/bash 2 | 3 | for VAR in PREVIOUS_PARASITE_STAGING_MYSQL \ 4 | PARASITE_CONF \ 5 | PARASITE_SCRATCH 6 | do 7 | if [ -z $(eval "echo \$$VAR") ]; then 8 | echo "$VAR must be set in your environment before running $0" 9 | exit 254 10 | fi 11 | done 12 | 13 | # bale out immediately on error 14 | set -e 15 | printf "{ 16 | \"datacheck_params\" : { 17 | \"registry_file\" : null, 18 | \"server_uri\" : null, 19 | \"old_server_uri\" : [\"$(${PREVIOUS_PARASITE_STAGING_MYSQL} details url)\"] 20 | }, 21 | \"history_file\" : null, 22 | \"output_dir\" : \"${PARASITE_SCRATCH}/datachecks/\", 23 | \"output_file\" : null 24 | }" > ${PARASITE_CONF}/datachecks_config.json -------------------------------------------------------------------------------- /parasite/scripts/production/fixes_patches/staging_patch_pull526/db_correspondance.tsv: -------------------------------------------------------------------------------- 1 | ascaris_suum_prjna62057_core_16_101_1 ascaris_suum_core_54_107_1 2 | hymenolepis_microstoma_prjeb124_core_16_101_1 hymenolepis_microstoma_core_54_107_1 3 | necator_americanus_prjna72135_core_16_101_1 necator_americanus_core_54_107_1 4 | schistosoma_mansoni_prjea36577_core_16_101_1 schistosoma_mansoni_core_54_107_1 5 | -------------------------------------------------------------------------------- /parasite/scripts/production/fixes_patches/staging_patch_pull526/hymenolepis_microstoma_core_54_107_1.sql: -------------------------------------------------------------------------------- 1 | use hymenolepis_microstoma_core_54_107_1; 2 | UPDATE gene SET description="Tubulin beta chain [Source:UniProtKB/TrEMBL;Acc:G3JWY8]" WHERE stable_id="HmN_003028780"; 3 | UPDATE gene SET description="Dicer [Source:UniProtKB/TrEMBL;Acc:H9C495]" WHERE stable_id="HmN_000252400"; 4 | UPDATE gene SET description="Ago1-like protein [Source:UniProtKB/TrEMBL;Acc:H9C496]" WHERE stable_id="HmN_000658200"; 5 | UPDATE gene SET description="60S ribosomal protein L28 [Source:UniProtKB/TrEMBL;Acc:G3JWY7]" WHERE stable_id="HmN_000911300"; 6 | -------------------------------------------------------------------------------- /parasite/scripts/production/get_bioproject.py: -------------------------------------------------------------------------------- 1 | #!/hps/software/users/wormbase/parasite/shared/.pyenv/versions/p395/bin/python 2 | 3 | import sys 4 | import os 5 | import re 6 | 7 | args = sys.argv 8 | 9 | core_db = args[1] 10 | 11 | if len(args)<2: 12 | print("Usage: python get_bioproject.py core_db\nExample: python get_bioproject.py ancylostoma_ceylanicum_prjna231479_core_17_105_1") 13 | raise ValueError 14 | 15 | try: 16 | bioproject = re.search("(prj[edbna]+\d+)_core", core_db).group(1) 17 | print(bioproject) 18 | except AttributeError: 19 | print("") 20 | 21 | 22 | -------------------------------------------------------------------------------- /parasite/scripts/production/get_ftp_bioproject.py: -------------------------------------------------------------------------------- 1 | #!/hps/software/users/wormbase/parasite/shared/.pyenv/versions/p395/bin/python 2 | 3 | import sys 4 | import os 5 | import re 6 | 7 | args = sys.argv 8 | 9 | core_db = args[1] 10 | 11 | if len(args)<2: 12 | print("Usage: python get_bioproject.py core_db\nExample: python get_bioproject.py ancylostoma_ceylanicum_prjna231479_core_17_105_1") 13 | raise ValueError 14 | 15 | bioproject_raw = core_db.split("_")[2] 16 | 17 | if re.match("^prj[edbna]+\d+", bioproject_raw): 18 | bioproject = bioproject_raw 19 | else: 20 | try: 21 | bioproject_match = re.search("^([^_]+)(prj[edbna]+\d+)", bioproject_raw) 22 | bioproject = bioproject_match.group(1) + "_" + bioproject_match.group(2) 23 | except AttributeError: 24 | print(core_db+"-----------ERROR-----------") 25 | 26 | print(bioproject) -------------------------------------------------------------------------------- /parasite/scripts/production/ncbi/assemblies_for_taxon.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | use strict; 3 | use warnings; 4 | use feature 'say'; 5 | 6 | for my $taxon (@ARGV){ 7 | say for get_assemblies_for_taxon($taxon); 8 | } 9 | 10 | sub get_assemblies_for_taxon { 11 | my ($taxon) = @_; 12 | my @result; 13 | local $/ = "--"; 14 | open(my $fh, "curl -s 'https://www.ncbi.nlm.nih.gov/assembly/organism/browse-organism/$taxon/all/?p\$l=Ajax&page=1&pageSize=1000&sortCol=4&sortDir=-1' | grep -B 2 href |"); 15 | while(<$fh>){ 16 | my ($accession) = /.*?/dev/null 2>&1 && pwd )" 4 | rm -rf $DIR/tmp 5 | mkdir $DIR/tmp 6 | $DIR/assemblies_for_taxon.pl 6157 6231 \ 7 | | tee $DIR/tmp/assemblies_for_taxon.out \ 8 | | $DIR/doc_for_assembly.pl \ 9 | | tee $DIR/tmp/doc_for_assembly.out\ 10 | | $DIR/compare_docs_against_current_staging.pl \ 11 | | tee $DIR/tmp/compare_docs_against_current_staging.out \ 12 | | perl -MHash::Merge -MYAML -e 'local $/; my @docs = Load(<>); my $o = {};$o = Hash::Merge::merge($o, $_) for @docs; print Dump $o;' \ 13 | | tee $DIR/tmp/result.out 14 | -------------------------------------------------------------------------------- /parasite/scripts/production/nextflow/modules/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/parasite/scripts/production/nextflow/modules/README.md -------------------------------------------------------------------------------- /parasite/scripts/production/nextflow/modules/busco/busco_genome_factory.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/parasite/scripts/production/nextflow/modules/busco/busco_genome_factory.nf -------------------------------------------------------------------------------- /parasite/scripts/production/nextflow/modules/omark/omamer_hog.nf: -------------------------------------------------------------------------------- 1 | process OMAMER_HOG { 2 | 3 | label 'omamer' 4 | 5 | input: 6 | file protein 7 | val outdir 8 | val db 9 | val augustus_species 10 | val odb 11 | 12 | output: 13 | path "proteins.omamer", emit: omamer_file 14 | val outdir, emit:species_outdir 15 | val db 16 | 17 | // ourdir is Salmo_trutta (production name) 18 | publishDir "${params.output_dir}/${outdir}/", mode: 'copy' 19 | 20 | script: 21 | """ 22 | omamer search --db ${params.omamer_database} --query ${protein} --score sensitive --out proteins.omamer 23 | """ 24 | } -------------------------------------------------------------------------------- /parasite/scripts/production/nextflow/modules/omark/run_omark.nf: -------------------------------------------------------------------------------- 1 | process RUN_OMARK { 2 | 3 | label 'omamer' 4 | 5 | input: 6 | file omamer_file 7 | val outdir 8 | val db 9 | 10 | 11 | output: 12 | path("omark_output/proteins.sum"), emit: summary_file 13 | val outdir, emit:species_outdir 14 | val db 15 | 16 | publishDir "${params.output_dir}/${outdir}/", mode: 'copy' 17 | 18 | script: 19 | """ 20 | omark -f ${omamer_file} -d ${params.omamer_database} -o omark_output 21 | """ 22 | } -------------------------------------------------------------------------------- /parasite/scripts/production/nextflow/subworkflows/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/parasite/scripts/production/nextflow/subworkflows/README.md -------------------------------------------------------------------------------- /parasite/scripts/production/nextflow/subworkflows/busco_dataset/main.nf: -------------------------------------------------------------------------------- 1 | // Import modules 2 | include { BUSCO_ODB } from '../../modules/busco/busco_dataset.nf' 3 | include { BUSCO_AUGUSTUS_SPECIES } from '../../modules/busco/busco_dataset.nf' 4 | 5 | // Run main workflow 6 | -------------------------------------------------------------------------------- /parasite/scripts/production/rnaseq/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/parasite/scripts/production/rnaseq/__init__.py -------------------------------------------------------------------------------- /parasite/scripts/production/variation/gaf_file_validator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/parasite/scripts/production/variation/gaf_file_validator.py -------------------------------------------------------------------------------- /parasite/scripts/production/variation/id_to_external_db_name.py: -------------------------------------------------------------------------------- 1 | #!/hps/software/users/wormbase/parasite/shared/.pyenv/versions/production-tools/bin/python 2 | 3 | idregex_to_db = { 4 | '^WBVar\d{8}$' : 'WORMBASE_VARIATION', 5 | '^WBRNAi\d{8}$' : 'WORMBASE_RNAI', 6 | '^RNAi$' : 'RNAi_STUDY' 7 | } -------------------------------------------------------------------------------- /parasite/scripts/production/xref/afdb_name_check.sh: -------------------------------------------------------------------------------- 1 | for species_path in $(ls -1 -d ${PARASITE_SCRATCH}/alphafold/WBPS${PARASITE_VERSION}/*_*_*); 2 | do species=$(basename ${species_path}); 3 | afdb_pf_count=$($PARASITE_STAGING_MYSQL $cdb -Ne "SELECT COUNT(*) FROM protein_feature t1 JOIN analysis t2 ON t1.analysis_id=t2.analysis_id WHERE t2.logic_name='alphafold_import';") 4 | echo "Found ${afdb_pf_count} AlphaFold protein features in $cdb"; 5 | $PARASITE_STAGING_MYSQL $cdb -Ne "SELECT hit_description FROM protein_feature t1 JOIN analysis t2 USING(analysis_id) WHERE t2.logic_name='alphafold_import' GROUP BY translation_id HAVING COUNT(translation_id)>1;" | while read mres; 6 | do printf "${species}\t${mres}\n" >> $duplicated_translations_file; 7 | done; 8 | printf "Done\n\n"; 9 | fi; 10 | done -------------------------------------------------------------------------------- /parasite/scripts/production/xref/ini_to_species.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | use Config::IniFiles; 3 | 4 | my @ans; 5 | my $cfg = Config::IniFiles->new( -file => @ARGV ? @ARGV[0] : STDIN ); 6 | die unless $cfg; 7 | for my $section ( grep /species/, $cfg->Sections ) { 8 | for my $name (split ", " , $cfg->val( $section, "aliases")){ 9 | if ( grep /wormbase/, $cfg->val( $section, "source" ) ) { 10 | print "$name\twormbase\n"; 11 | } 12 | else { 13 | print "$name\tparasite\n"; 14 | } 15 | } 16 | } 17 | -------------------------------------------------------------------------------- /scripts/BLAST_scripts/gff2cds.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | 3 | # ms2@sanger.ac.uk 4 | 5 | # extracts the start and end coordinates of all the sequences from a gff file having the cds tag associated 6 | # with their "exon's". 7 | # the possible second fields of the gff file were: hand_built, Genefinder, stl, stl-preliminary, Coding, assembly-default. 8 | # now, we have only curated and preliminary 9 | 10 | 11 | use strict; 12 | 13 | my %line; my %cds; 14 | 15 | while (<>) { 16 | chomp; 17 | if ((/^\S+\t(curated)\tCDS\t/) && (/\"(\S+\.\S+)\"/)) { 18 | print "$_\n"; 19 | } 20 | # if ((/^\S+\t+\w*\tCDS\t/) && (/\"(\S+\.\S+)\"$/)) { 21 | # $cds{$1} = "yes"; 22 | # } 23 | } 24 | 25 | #foreach (keys (%line)) { 26 | # if (exists $cds{$_}) { 27 | # print "$line{$_}\n"; 28 | # } 29 | #} 30 | -------------------------------------------------------------------------------- /scripts/BLAST_scripts/gff2cos.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | 3 | # ms2@sanger.ac.uk 4 | 5 | # extracts the lines from a worm acedb gff file being either cosmids or yacs 6 | 7 | use strict; 8 | 9 | while (<>) { 10 | chomp; 11 | if ((/^\S+\tGenomic_canonical\tregion\s+/) && (/\"(\S+)\"$/)) { 12 | print "$_\n"; 13 | } 14 | elsif ((/^\S+\tLink\tregion\s+/) && (/\"(\S+)\"$/)) { 15 | print "$_\n"; 16 | } 17 | } 18 | 19 | -------------------------------------------------------------------------------- /scripts/BLAST_scripts/make_humanpepfile.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/ensembl/bin/perl 2 | 3 | # converts ensembl.pep file with human peptide entries into ace file 4 | 5 | use strict; 6 | 7 | while (<>) { 8 | if (/\>(ENS\S+)/) { 9 | print "\nProtein : \"ENSEMBL:$1\"\n"; 10 | print "Peptide \"ENSEMBL:$1\"\n"; 11 | print "Species \"Homo sapiens\"\n"; 12 | print "Database \"Ensembl\" \"$1\" \"$1\"\n\n"; 13 | print "Peptide : \"ENSEMBL:$1\"\n"; 14 | } 15 | else { 16 | print $_; 17 | } 18 | } 19 | 20 | __END__ 21 | Protein : "ENSEMBL:ENSP00000266127" 22 | Peptide "ENSEMBL:ENSP00000266127" 23 | Species "Homo sapiens" 24 | Database "Ensembl" "ENSP00000266127" "ENSP00000266127" 25 | 26 | Peptide : "ENSEMBL:ENSP00000266127" 27 | AFYPPRLFAPPPPWFFPPISPP 28 | -------------------------------------------------------------------------------- /scripts/BLAST_scripts/map_gff_fails.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/perl 2 | 3 | use lib $ENV{'CVS_DIR'}; 4 | use Coords_converter; 5 | use Wormbase; 6 | 7 | my $wormbase = Wormbase->new; 8 | my $database = $wormbase->autoace;; 9 | 10 | #CHROMOSOME_I waba_coding similarity 7504218 7504560 378.0000 - . Target "Sequence:cb25.fpc2695" 196866 197208 197208,7504218,0 11 | 12 | my $coords = Coords_converter->invoke("$database"); 13 | #my $coords = Coords_converter->invoke(); 14 | 15 | while(<>) { 16 | chomp; 17 | my @data = split(/\t/,$_); 18 | my @clone_coords = $coords->LocateSpan($data[0], $data[3], $data[4]); 19 | 20 | $data[0] = $clone_coords[0]; 21 | $data[3] = $clone_coords[1]; 22 | $data[4] = $clone_coords[2]; 23 | 24 | print join("\t",@data),"\n"; 25 | } 26 | -------------------------------------------------------------------------------- /scripts/ENSEMBL/etc/njtree.12.worm_compara_test_orthotree.nh: -------------------------------------------------------------------------------- 1 | (((((((((((6238*,497829)6231,31234)6231,(135651,886184)6231)6231,6239*)6231,281687)6231,96668)6231,54126)6231,(6305,(34506,(6233,6326))6231)6231)6231,(6289,37862)6231)6231,(((6279,7209)6231,6233)6231,6253)6231)6231,6334))6231; 2 | -------------------------------------------------------------------------------- /scripts/ENSEMBL/lib/WormFeature.pm: -------------------------------------------------------------------------------- 1 | # stub to import stuff 2 | use WormFeature::Blat; 3 | use WormFeature::WublastX; 4 | 1; 5 | -------------------------------------------------------------------------------- /scripts/ENSEMBL/scripts/split_wig.pl: -------------------------------------------------------------------------------- 1 | #!/software/worm/perl_510/bin/perl 2 | # takes a .wig file and spltis it by every thousand sequences 3 | # appends a .#number 4 | 5 | use strict; 6 | 7 | my $c=1; 8 | my $f=$ARGV[0]; 9 | open(my $outf,">","$f.$c"); 10 | 11 | while (<>){ 12 | if ( /^track/ && ($c++ % 1000)== 0){ 13 | close $outf; 14 | open($outf,">","$f.$c") || die @!; 15 | } 16 | print $outf $_; 17 | } 18 | -------------------------------------------------------------------------------- /scripts/ENSEMBL/tests/wormy.t: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | use FindBin; 3 | use lib "$FindBin::Bin/../lib"; 4 | use strict; 5 | use warnings; 6 | use Test::More 'no_plan'; 7 | use Wormy; 8 | use YAML; 9 | 10 | use constant INFILE => 'test.gff'; 11 | 12 | ok(1,'test Test::More'); 13 | ok(Wormy->new,'new Wormy'); 14 | my $testworm=Wormy->new; 15 | ok($testworm->get_lines(INFILE),'trying to parse the file'); 16 | ok($testworm->parse_lines,'parsing into lvl1 features'); 17 | 18 | print YAML::DumpFile('test.yml',$testworm); 19 | -------------------------------------------------------------------------------- /scripts/GENEACE/Update_Biotype.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/scripts/GENEACE/Update_Biotype.pl -------------------------------------------------------------------------------- /scripts/GENEACE/update_geneace.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/scripts/GENEACE/update_geneace.pl -------------------------------------------------------------------------------- /scripts/MISC_SCRIPTS/test.remapwig.pl: -------------------------------------------------------------------------------- 1 | use lib $ENV{'CVS_DIR'}."/Modules"; 2 | use Remap_wig; 3 | 4 | my $mapper = Remap_wig->new('elegans'); 5 | my $file = '/nfs/team71/worm/ar2/Desktop/RNAPIIIP2_dyeswap_WS180.wig'; 6 | $mapper->remap_file ('wig' => $file, 7 | 'genome' => 'I', 8 | 'out' => $file."_remap", 9 | 'old' => 140, 10 | 'new' => 200, 11 | ); 12 | -------------------------------------------------------------------------------- /scripts/MISC_SCRIPTS/uniquify_fasta.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl5.8.0 -w 2 | 3 | my $pep; 4 | while (<>) { 5 | if (/\>(\w+)/ ) { 6 | $pep = $1; 7 | $peps{$pep} = ""; 8 | } 9 | else { 10 | $peps{$pep} .= $_; 11 | } 12 | } 13 | 14 | foreach (sort keys %peps) { 15 | print "\>$_\n$peps{$_}"; 16 | } 17 | 18 | 19 | =pod 20 | 21 | =head1 NAME 22 | 23 | uniquify_fasta.pl 24 | 25 | Very simple script to make a version of a fasta file unique ie no duplicate entries. 26 | 27 | Use like this 28 | 29 | WS123.pep | perl uniquify_fasta.pl > WS123.pep.unique 30 | 31 | =cut 32 | -------------------------------------------------------------------------------- /scripts/TESTS/CarryOver.pl: -------------------------------------------------------------------------------- 1 | #!/software/bin/perl -w 2 | 3 | use lib $ENV{'CVS_DIR'}; 4 | use Wormbase; 5 | use Storable; 6 | use Log_files; 7 | use Modules::CarryOver; 8 | use Getopt::Long; 9 | 10 | my ($store, $old, $new); 11 | my ($pep, $rna); 12 | GetOptions ( 13 | "old:i" => \$old, 14 | "new:i" => \$new, 15 | "store:s" => \$store, 16 | "pep" => \$pep, 17 | "rna" => \$rna 18 | ); 19 | 20 | die("need store old(int) and new(int)\n") unless ($store and $old and $new); 21 | my $wormbase = retrieve( $store ); 22 | $wormbase->debug('ar2'); 23 | my $log = Log_files->make_build_log($wormbase); 24 | 25 | my $carry = CarryOver->new($wormbase,$log); 26 | $carry->carry_wormpep($new, $old) if $pep; 27 | $carry->carry_wormrna($new, $old) if $rna; 28 | 29 | $log->write_to("done\n"); 30 | $log->mail; 31 | exit; 32 | -------------------------------------------------------------------------------- /scripts/Transposon_sync.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/scripts/Transposon_sync.pl -------------------------------------------------------------------------------- /scripts/agp2fpc.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl -w 2 | 3 | use strict; 4 | 5 | while (<>) { 6 | my @f = split /\t/; 7 | if ($f[4] !~ /N/) { 8 | chomp; 9 | print $_, "\t", $f[5]."_C", "\t", $f[1], "\t", $f[2], "\n"; 10 | } 11 | elsif ($f[4] =~ /N/) { 12 | s/[+-]//; 13 | print $_; 14 | } 15 | else { 16 | print "Problem!\n"; 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /scripts/checkLongText.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | 3 | while (<>){ 4 | if (/^LongText : "(.+)"/) { 5 | if ($inside) { print "non-termination line $.: $1 inside $inside\n" ; } 6 | else { $inside = $1 ; } 7 | } 8 | elsif (/^LongText/) { 9 | chop ; 10 | print "wierd line $.: $_" ; 11 | if ($inside) { print " inside $inside" ; } 12 | print "\n" ; 13 | } 14 | if (/^\*\*\*LongTextEnd\*\*\*\n$/) { undef $inside ; } 15 | } 16 | -------------------------------------------------------------------------------- /scripts/check_superlinks.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | 3 | 4 | 5 | # get data from camace 6 | 7 | use Ace ; 8 | $campath = "/wormsrv2/camace" ; 9 | $camdb = Ace->connect(-path=>"$campath") || 10 | die "failed to connect to database\n" ; 11 | 12 | # then some info about current links 13 | 14 | $it = $camdb->fetch_many(Sequence => 'SUPERLINK*') ; 15 | while ($obj = $it->next) { 16 | 17 | print "\nSUPERLINK object : \'$obj\'\n"; 18 | foreach $a ($obj->at('Structure.Subsequence')) { 19 | ($seq, $start, $end) = $a->row ; 20 | print " $seq \t$start -> $end\n"; 21 | 22 | if ($seq =~ /\./) { 23 | print "CDS object in SUPERLINK. Abort \'makelinks\' \n"; 24 | # exit; 25 | } 26 | 27 | } 28 | } 29 | 30 | 31 | exit; 32 | 33 | 34 | -------------------------------------------------------------------------------- /scripts/confirm_genes.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WormBase/wormbase-pipeline/cdf8de250768bf7c4d20fb50d159c7c1b50d25af/scripts/confirm_genes.pl -------------------------------------------------------------------------------- /scripts/dbfetch.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | # 3 | # dbfetch 4 | # 5 | # Usage: dbfetch 6 | # 7 | # Last edited by: $Author: ar2 $ 8 | # Last edited on: $Date: 2005-12-16 11:18:55 $ 9 | 10 | 11 | my $database = shift; 12 | my $file = shift; 13 | my $seq = ""; 14 | 15 | $/=">"; 16 | 17 | open (SHOTGUN, "<$database"); 18 | while () { 19 | chop $_; 20 | /^(\S+)\s+(\S+)/; 21 | if (($file eq $1) || ($file eq $2)) { 22 | $seq = $_; 23 | last; 24 | } 25 | } 26 | close SHOTGUN; 27 | 28 | $/="\n"; 29 | 30 | print ">$seq\n"; 31 | 32 | exit(0); 33 | -------------------------------------------------------------------------------- /scripts/download_human_IPI.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl5.6.1 -w 2 | # 3 | # download_human_IPI.pl 4 | # 5 | # by Chao-Kung Chen 6 | # 7 | # Script to run consistency checks on the geneace database 8 | # 9 | # Last updated by: $Author: gw3 $ 10 | # Last updated on: $Date: 2010-04-29 14:29:59 $ 11 | 12 | 13 | use strict; 14 | 15 | my $rundate = `date +%m_%d`; chomp $rundate; 16 | 17 | chdir "/lustre/scratch101/ensembl/wormpipe/BlastDB"; 18 | 19 | `wget ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.fasta.gz`; 20 | 21 | system("gunzip ipi.HUMAN.fasta.gz; mv ipi.HUMAN.fasta ipi_human_$rundate"); 22 | 23 | exit(0); 24 | 25 | 26 | -------------------------------------------------------------------------------- /scripts/dump_clustal.tcsh: -------------------------------------------------------------------------------- 1 | rm -f /nfs/wormpub/BUILD/autoace/wormpep_clw.sql.gz 2 | /software/worm/postgres/bin/pg_dump --inserts -x -O -t clustal -h pgsrv1 -p 5436 -U worm_clw -t clustal worm_clw |perl ~wormpub/wormbase/scripts/p2msql.pl | gzip -9 -c > /nfs/wormpub/BUILD/autoace/MISC_OUTPUT/wormpep_clw.sql.gz 3 | -------------------------------------------------------------------------------- /scripts/fasta2samelength_0.2: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | 3 | $file = shift; 4 | $linelen = shift||60; 5 | $nextline = $linelen - 1; 6 | 7 | open (FILE, "<$file"); 8 | while () { 9 | if (/^>/) { 10 | $count=0; 11 | for ($x=0;$x<=$#sequence;$x++) { 12 | print $sequence[$x]; 13 | if ($count==$nextline) {print "\n";$count=0;} else {$count++;} 14 | } 15 | if ($count !=0) {print "\n";} 16 | undef @sequence; 17 | print; 18 | } 19 | 20 | else {s/\n//;s/\s+//g; 21 | undef @newline; 22 | @newline=split(//,$_); 23 | push(@sequence,@newline); 24 | } 25 | 26 | } 27 | close FILE; 28 | 29 | #print out last entry 30 | $count=0; 31 | for ($x=0;$x<=$#sequence;$x++) { 32 | print $sequence[$x]; 33 | if ($count==$nextline) {print "\n";$count=0;} else {$count++;} 34 | } 35 | print "\n"; 36 | 37 | 38 | 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /scripts/geneprediction_utility_scripts/cds2transcripts.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | 3 | while (<>){ 4 | s/CDS :/Transcript :/; 5 | next if /^CDS|^Evidence|^Remark|^Predicted|Start_not_found|End_not_found|Genetic_code|^Brief_identification/; 6 | s/Corresponding_transcript/Corresponding_CDS/; 7 | s/curated/Coding_transcript/; 8 | print; 9 | } 10 | -------------------------------------------------------------------------------- /scripts/geneprediction_utility_scripts/rename_cds.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | # rename CDSes, so the longest one is a 3 | 4 | use Ace; 5 | use Ace::Sequence; 6 | 7 | my $db=Ace->connect(-path => shift); 8 | 9 | my @suffix=qw(a b c d e f g h i j k l m n o p q r s t u v w x y z); 10 | 11 | my $it = $db->fetch_many(Gene => '*'); 12 | while (my $gene = $it->next){ 13 | next unless $gene->Corresponding_CDS; 14 | my @CDSes = $gene->Corresponding_CDS; 15 | my $n=0; 16 | foreach my $cds (sort {Ace::Sequence->new($b)->length() <=> Ace::Sequence->new($a)->length()} @CDSes){ 17 | my $cname; 18 | if (scalar(@CDSes) == 1){ 19 | $cname = $gene->Sequence_name; 20 | }else{ 21 | $cname = $gene->Sequence_name . $suffix[$n]; 22 | $n++; 23 | } 24 | print "-R CDS : $cds _$cname\n" unless $cname eq $cds; 25 | } 26 | } 27 | -------------------------------------------------------------------------------- /scripts/get_CRC64_checksum.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl5.6.0 2 | 3 | # Chao-kung Chen 4 | # July 29, 2002 @ recorded temperature 30 degree Celcius 5 | # What it does: get CRC64 checksum appeared in SQ line of SwissProt flatflie 6 | # This script revises Dan's get_checksum.pl, which generates GCG checksum 7 | 8 | 9 | use lib "/wormsrv2/scripts"; 10 | use CRC64; 11 | 12 | my $file = shift; 13 | my $seq = ""; 14 | my $name = ""; 15 | 16 | 17 | open (SEQ, "<$file") or die "Can't open sequence file $!\n"; 18 | while () { 19 | chomp; 20 | if (/^>(\S+)/) { 21 | $name = $1; 22 | next; 23 | } 24 | $seq .= $_; 25 | } 26 | close SEQ; 27 | 28 | # lower to upper-case 29 | $seq =~ tr/a-z/A-Z/; 30 | 31 | $crc = SWISS::CRC64::crc64("$seq"); #returns a string like "E3DCADD69B01ADD1" 32 | 33 | print "CRC64_checksum: $crc\n"; 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /scripts/get_chromosome.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | # dl 3 | # 991118 4 | # 5 | # hacked from one of Steve's subroutines 6 | 7 | 8 | $project=shift; 9 | $exec="tace /nfs/disk100/wormpub/acedb/ace4/autoace"; 10 | 11 | $command=<) { 19 | if (/^Interpolated_gMap\s+\"(\S+)"\s+/) { 20 | print "$project is located on chromosome $1\n"; 21 | } 22 | } 23 | close TEXTACE; 24 | 25 | exit; 26 | -------------------------------------------------------------------------------- /scripts/get_wormpep_annotations_from_swiss_prot: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | 3 | open(swissprot,"getz -f 'acc def' \"[swissprot-org:Caenorhabditis elegans] < wormpep\"|"); 4 | 5 | while () {#print; 6 | if (/^AC\s+(\S+);/) {$swissprot=$1;push(@swiss,$1);} 7 | if (/^DE\s+(.+)/) {$def{$swissprot}=$def{$swissprot}.$1;} 8 | 9 | } 10 | 11 | close swissprot; 12 | 13 | foreach $protein (@swiss) { 14 | 15 | open(swissprot,"getz -t \"wormpep < [swissprot-acc:$protein]\"|"); 16 | while() { 17 | if (/>\S+\s+(CE\d+)/) {print "\nProtein WP:$1\nDB_remark \"$def{$protein}\"\n";} 18 | } 19 | #print "Sequence"; 20 | 21 | } 22 | 23 | -------------------------------------------------------------------------------- /scripts/gff_sort: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | 3 | while (<>) { 4 | s/#.*//; 5 | next unless /\S/; 6 | @f = split /\t/; 7 | push @a, $_; 8 | push @n, $f[0]; 9 | push @s, $f[3]; 10 | push @e, $f[4]; 11 | } 12 | 13 | foreach $i (sort { $n[$a] cmp $n[$b] or $s[$a] <=> $s[$b] or $e[$a] <=> $e[$b] } 0..$#a) { 14 | print $a[$i]; 15 | } 16 | 17 | exit(0); 18 | -------------------------------------------------------------------------------- /scripts/hmmfs2ace2: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | #to parse the output of hmmfs to ace format 3 | #950203 4 | #Steven Jones 5 | 6 | 7 | if ($#ARGV != 2) {print "usage: hmmfs2ace2 outputfile threshold repeatname\n";} 8 | 9 | open (output, "$ARGV[0]"); 10 | 11 | 12 | while () { 13 | 14 | 15 | 16 | 17 | if (/(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)/) { 18 | 19 | if ($1 >= $ARGV[1]) { 20 | 21 | print "Sequence $6\n";$i=1; 22 | print "Homol $ARGV[2] hmmfs.2 $1 $2 $3 $4 $5\n\n"; 23 | 24 | print "Sequence $ARGV[2]\n"; 25 | if ($3 > $2) {print "Homol $6 hmmfs.2 $1 $4 $5 $2 $3 \n\n" } 26 | else {print "Homol $6 hmmfs.2 $1 $5 $4 $3 $2 \n\n" } 27 | 28 | } 29 | 30 | 31 | } 32 | } 33 | 34 | -------------------------------------------------------------------------------- /scripts/hmmfs2ace2_4: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | #to parse the output of hmmfs to ace format 3 | #950203 4 | #Steven Jones 5 | 6 | 7 | if ($#ARGV != 2) {print "usage: hmmfs2ace2 outputfile threshold repeatname\n";} 8 | 9 | open (output, "$ARGV[0]"); 10 | 11 | 12 | while () { 13 | 14 | 15 | 16 | 17 | if (/(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)/) { 18 | 19 | if ($1 >= $ARGV[1]) { 20 | 21 | print "\nSequence $6\n";$i=1; 22 | print "Homol Motif_homol $ARGV[2] hmmfs.3 $1 $2 $3 $4 $5\n\n"; 23 | 24 | print "Motif $ARGV[2]\n"; 25 | if ($3 > $2) {print "Homol DNA_homol $6 hmmfs.3 $1 $4 $5 $2 $3 \n\n" } 26 | else {print "Homol DNA_homol $6 hmmfs.3 $1 $5 $4 $3 $2 \n\n" } 27 | 28 | } 29 | 30 | 31 | } 32 | } 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /scripts/ortholog/ladeanna.rb: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env ruby 2 | # that is a small one-off script to parse Ladeanna's C.briggsae orthologs 3 | 4 | def read_common_data(file) 5 | eval File.new("/nfs/disk100/wormpub/DATABASES/current_DB/COMMON_DATA/#{file}",'r') 6 | return $VAR1 7 | end 8 | 9 | def print_ace(gene1,gene2,organism2) 10 | puts "Gene : \"#{gene1}\"" 11 | puts "Ortholog #{gene2} \"#{organism2}\" Paper_evidence WBPaper00038778","" 12 | end 13 | 14 | cds2gene = read_common_data("cds2wbgene_id.dat") 15 | 16 | ARGF.each{|line| 17 | line.chomp! 18 | columns = line.split(',') 19 | briggsae_gene = cds2gene[columns[4]] 20 | elegans_gene = cds2gene[columns[10]] 21 | next if briggsae_gene.nil? ||elegans_gene.nil? 22 | print_ace(elegans_gene,briggsae_gene,'Caenorhabditis briggsae') 23 | print_ace(briggsae_gene,elegans_gene,'Caenorhabditis elegans') 24 | } 25 | 26 | -------------------------------------------------------------------------------- /scripts/parse_history.pl: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | 3 | 4 | 5 | $history = shift; 6 | %genes = (); 7 | 8 | 9 | open (HISTORY, "<$history"); 10 | while () { 11 | 12 | undef ($id); 13 | undef ($acc); 14 | undef ($start); 15 | undef ($end); 16 | undef ($changes); 17 | 18 | chomp; 19 | 20 | ($id,$acc,$start,$end) = split (/\t/,$_); 21 | 22 | $current = $genes{$id}; 23 | $current++; 24 | $genes{$id} = $current; 25 | 26 | 27 | 28 | } 29 | close HISTORY; 30 | 31 | 32 | foreach $key (keys %genes) { 33 | 34 | print "$key \t: $genes{$key}\n"; 35 | 36 | 37 | } 38 | 39 | exit(0); 40 | -------------------------------------------------------------------------------- /scripts/pfetch_gene: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl5.6.1 -w 2 | 3 | my $gene = shift; 4 | unless ($gene) { 5 | print "enter gene . .\n"; 6 | $gene = ; 7 | chomp $gene; 8 | } 9 | 10 | $gene =~ /(\w+)\.\w+/; 11 | my $clone = $1; 12 | 13 | my $acc = `grep $clone /nfs/users/nfs_w/wormpub/DATABASES/current_DB/COMMON_DATA/accession2clone.dat`; 14 | my @data = split(/\s+/,$acc); 15 | print `pfetch -F $data[1] | less`; 16 | 17 | 18 | __END__ 19 | 20 | =pod 21 | 22 | =head2 NAME - pfetch_gene 23 | 24 | 25 | =head1 USAGE 26 | 27 | =over 4 28 | 29 | 30 | pfetch_name gene 31 | eq pfetch_gene AH6.1a will pfetch the record for clone AH6. 32 | The accession is looked up from the file ~wormpipe/dumps/accession2clone.txt 33 | 34 | 35 | This utility is to quickly pfetch the clone EMBL record for any particular gene. 36 | -------------------------------------------------------------------------------- /scripts/pfscanpdb: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | # 3 | # Wrapper to pfscanp to search protein databases. 4 | # 5 | # 6 | open(proteins,"$ARGV[0]"); 7 | 8 | while () { 9 | if (/>(\S+)/) {$sequence=$1;push(@sequences,$1);} else {s/[^a-zA-Z\n]//g;} 10 | $sequence{$1}=$sequence{$1}.$_; 11 | } 12 | 13 | 14 | foreach $peptide (@sequences) { 15 | open(temp,">/tmp/temppfscanpdb$$"); 16 | print temp $sequence{$peptide}; 17 | close temp; 18 | open(pfscanp,"pfscanp -a /tmp/temppfscanpdb$$ |"); 19 | while () {print;} 20 | } 21 | 22 | unlink '/tmp/temppfscanpdb$$' 23 | 24 | -------------------------------------------------------------------------------- /scripts/rewrap: -------------------------------------------------------------------------------- 1 | #!/software/bin/perl 2 | 3 | my $initial = 0; 4 | my $seq; 5 | 6 | # load strung to memory 7 | my $file = shift; 8 | 9 | open (FASTA, "<$file"); 10 | while () { 11 | chomp; 12 | if (/^>(\S+.+)/) { 13 | &rewrite($seq) unless ($initial == 0); 14 | print ">$1\n"; 15 | $initial++; 16 | $seq = ""; 17 | next; 18 | } 19 | $seq .= $_; 20 | } 21 | close FASTA; 22 | 23 | &rewrite($seq); 24 | 25 | exit(0); 26 | 27 | 28 | 29 | sub rewrite { 30 | my $seq = shift; 31 | $size = length ($seq); 32 | $no_lines = int ($size / 60) +1; 33 | for ($i = 0; $i < $no_lines; $i++) { 34 | $linestart = $i * 60; 35 | $newline = substr($seq,$linestart,60); 36 | print "$newline\n"; 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /scripts/wee_gff_dump: -------------------------------------------------------------------------------- 1 | #!/bin/csh -f 2 | 3 | unlimit 4 | 5 | switch ($#argv) 6 | case "4": 7 | breaksw 8 | default: 9 | echo 'Usage: wee_gff_dump ' ; exit 1 10 | endsw 11 | 12 | 13 | #/software/worm/acedb/old_versions/giface $1 < /dev/null 14 | /software/worm/acedb/current/bin/giface $1 < /dev/null 15 | #gif seqget $2 ; seqdisplay; seqactions -gf_features; seqfeatures -version $4 -file $3 16 | gif seqget $2; seqfeatures -version $4 -file $3 17 | EOF 18 | 19 | 20 | -------------------------------------------------------------------------------- /wgf/newnem.atg: -------------------------------------------------------------------------------- 1 | // @(#)newnem.atg 1.2 8/23/94 2 | siteType: atg refSeqs: genes freqType: within classDef: unique 3 | startOff: -9 endOff: 11 numSymbs: 1 maxSymb: 5 numForced: 3 forcedPos: 0 1 2 jump: 1 4 | * 5 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 | 19 13 21 13 12 29 31 20 22 48 0 0 13 16 9 17 15 9 13 22 13 7 | 11 16 7 10 16 11 3 10 12 0 0 0 8 15 13 12 10 21 7 10 21 8 | 5 8 3 11 5 5 12 8 5 0 0 48 17 13 14 9 5 11 17 3 6 9 | 13 11 17 14 15 3 2 10 9 0 48 0 10 4 12 10 18 7 11 13 8 10 | -------------------------------------------------------------------------------- /wgf/tables: -------------------------------------------------------------------------------- 1 | // @(#)tables 1.2 8/23/94 2 | newnem.codon 3 | newnem.intron3 4 | newnem.intron5 5 | zk637.trinuc 6 | newnem.atg 7 | zk637.intron3 8 | zk637.intron5 9 | zk637.atg 10 | ref.hist 11 | -------------------------------------------------------------------------------- /wgf/zk637.atg: -------------------------------------------------------------------------------- 1 | // @(#)zk637.atg 1.2 8/23/94 2 | siteType: atg refSeqs: all freqType: within classDef: unique 3 | startOff: -9 endOff: 11 numSymbs: 1 maxSymb: 5 numForced: 3 forcedPos: 0 1 2 jump: 1 4 | * 5 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 | 26290 26290 26288 26288 26288 26287 26288 26289 26289 26290 26291 26293 26294 26294 26294 26295 26295 26294 26294 26294 26293 7 | 14385 14386 14387 14387 14386 14386 14386 14386 14385 14386 14387 14387 14388 14387 14388 14388 14387 14387 14387 14386 14388 8 | 14388 14386 14387 14387 14387 14388 14388 14387 14388 14387 14387 14386 14385 14386 14386 14386 14386 14387 14387 14386 14385 9 | 26293 26294 26294 26294 26295 26295 26294 26294 26294 26293 26291 26290 26289 26289 26288 26287 26288 26288 26288 26290 26290 10 | -------------------------------------------------------------------------------- /wquery/BLASTX_data.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-02-20_11:28:43 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 2 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Genome_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class ... 25 | Count 26 | From 1 27 | Tag Homol_data 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/CDSs_with_multiple_genes.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-08-02_11:55:56 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class elegans_CDS 18 | From 1 19 | Condition COUNT Gene >1 20 | 21 | Colonne 2 22 | Width 12 23 | Mandatory 24 | Visible 25 | Class 26 | Class Gene 27 | From 1 28 | Tag Gene 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/CommonData:CDS_Lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-04-28_12:44:55 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title CommonData:CDS_Lab 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle CDS 16 | Width 20 17 | Optional 18 | Visible 19 | Class 20 | Class elegans_CDS 21 | From 1 22 | Condition * 23 | 24 | Colonne 2 25 | Subtitle Lab 26 | Width 10 27 | Optional 28 | Visible 29 | Class 30 | Class Laboratory 31 | From 1 32 | Tag From_laboratory 33 | 34 | 35 | 36 | // End of these definitions 37 | -------------------------------------------------------------------------------- /wquery/CommonData:Clone_Type.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-07-20_13:15:45 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Subtitle Clone 14 | Width 15 15 | Optional 16 | Visible 17 | Class 18 | Class Clone 19 | From 1 20 | Condition Sequence 21 | 22 | Colonne 2 23 | Subtitle Type 24 | Width 15 25 | Mandatory 26 | Visible 27 | Next_Tag 28 | From 1 29 | Tag Type 30 | 31 | 32 | 33 | // End of these definitions 34 | -------------------------------------------------------------------------------- /wquery/CommonData:EST_Feature.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-04-28_13:36:05 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title CommonData:EST_Feature 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle Sequence 16 | Width 12 17 | Optional 18 | Visible 19 | Class 20 | Class Sequence 21 | From 1 22 | 23 | Colonne 2 24 | Subtitle Feature 25 | Width 12 26 | Mandatory 27 | Visible 28 | Class 29 | Class Feature 30 | From 1 31 | Tag Defines_feature 32 | 33 | 34 | 35 | // End of these definitions 36 | -------------------------------------------------------------------------------- /wquery/CommonData:Pseudogene_Lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-04-28_12:46:09 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title CommonData:Pseudogene_Lab 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle Pseudogene 16 | Width 20 17 | Optional 18 | Visible 19 | Class 20 | Class elegans_pseudogenes 21 | From 1 22 | Condition * 23 | 24 | Colonne 2 25 | Subtitle Lab 26 | Width 10 27 | Optional 28 | Visible 29 | Class 30 | Class Laboratory 31 | From 1 32 | Tag From_laboratory 33 | 34 | 35 | 36 | // End of these definitions 37 | -------------------------------------------------------------------------------- /wquery/CommonData:RNA_BriefID.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: pad 3 | // Date: 2012-01-25_14:59:25 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Transcript 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Text 26 | From 1 27 | Tag Brief_identification 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/CommonData:RNAgene_Lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-04-28_12:47:03 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title CommonData:RNAgene_Lab 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle RNA gene 16 | Width 20 17 | Optional 18 | Visible 19 | Class 20 | Class elegans_RNA_genes 21 | From 1 22 | Condition * 23 | 24 | Colonne 2 25 | Subtitle Lab 26 | Width 10 27 | Optional 28 | Visible 29 | Class 30 | Class Laboratory 31 | From 1 32 | Tag From_laboratory 33 | 34 | 35 | 36 | // End of these definitions 37 | -------------------------------------------------------------------------------- /wquery/DNA_homols.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2001-02-16_11:45:08 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Genome_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Hidden 24 | Show_Tag 25 | From 1 26 | Tag DNA_homol 27 | 28 | Colonne 3 29 | Width 12 30 | Optional 31 | Visible 32 | Class ... 33 | Count 34 | Right_of 2 35 | Tag DNA_homol 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/EST2feature.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-05-20_10:13:44 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Feature 26 | From 1 27 | Tag Defines_feature 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/EST_clone.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-06-17_14:46:42 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Clone 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Hidden 24 | Show_Tag 25 | From 1 26 | Tag cDNA 27 | 28 | Colonne 3 29 | Width 12 30 | Mandatory 31 | Visible 32 | Class 33 | Class Sequence 34 | From 1 35 | Tag Sequence 36 | Condition DNA 37 | 38 | 39 | 40 | // End of these definitions 41 | -------------------------------------------------------------------------------- /wquery/ESTacc2names.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2001-09-19_15:59:41 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Accession_number 18 | From 1 19 | 20 | Colonne 2 21 | Width 20 22 | Mandatory 23 | Visible 24 | Class 25 | Class Sequence 26 | From 1 27 | Tag Sequence 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/No_of_tm_domains.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-02-04_16:30:39 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Protein 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Method 26 | From 1 27 | Tag Feature 28 | Condition tmhmm 29 | 30 | Colonne 3 31 | Width 12 32 | Optional 33 | Visible 34 | Class ... 35 | Count 36 | Right_of 2 37 | 38 | 39 | 40 | // End of these definitions 41 | -------------------------------------------------------------------------------- /wquery/RNAgene2lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-04-21_11:39:53 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class elegans_RNA_genes 18 | From 1 19 | Condition * 20 | 21 | Colonne 2 22 | Width 12 23 | Optional 24 | Visible 25 | Class 26 | Class Laboratory 27 | From 1 28 | Tag From_laboratory 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/RNAi_dna.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: klh 3 | // Date: 2011-06-12_10:02:06 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class RNAi 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Text 25 | From 1 26 | Tag DNA_text 27 | 28 | Colonne 3 29 | Width 12 30 | Optional 31 | Visible 32 | Text 33 | Right_of 2 34 | Tag HERE 35 | 36 | 37 | 38 | // End of these definitions 39 | -------------------------------------------------------------------------------- /wquery/SCRIPT:CDS_status.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2008-04-23_14:49:35 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 30 14 | Optional 15 | Hidden 16 | Class 17 | Class Gene 18 | From 1 19 | Condition Live 20 | 21 | Colonne 2 22 | Width 30 23 | Optional 24 | Visible 25 | Class 26 | Class CDS 27 | From 1 28 | Tag Corresponding_CDS 29 | 30 | Colonne 3 31 | Width 30 32 | Optional 33 | Visible 34 | Next_Tag 35 | From 2 36 | Tag Prediction_status 37 | 38 | 39 | 40 | // End of these definitions 41 | -------------------------------------------------------------------------------- /wquery/SCRIPT:GeneGO_codes.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2010-07-07_11:18:13 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 14 14 | Optional 15 | Visible 16 | Class 17 | Class Gene 18 | From 1 19 | Condition GO_term 20 | 21 | Colonne 2 22 | Width 12 23 | Mandatory 24 | Visible 25 | Class 26 | Class GO_term 27 | From 1 28 | Tag GO_term 29 | 30 | Colonne 3 31 | Width 12 32 | Mandatory 33 | Visible 34 | Next_Tag 35 | Right_of 2 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/SCRIPT:GeneID_updater.pl.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-05-09_13:36:18 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title WBGeneID check 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle Gene 16 | Width 20 17 | Optional 18 | Visible 19 | Class 20 | Class Gene 21 | From 1 22 | 23 | Colonne 2 24 | Subtitle Seq_name 25 | Width 18 26 | Optional 27 | Visible 28 | Class 29 | Class Gene_name 30 | From 1 31 | Tag Sequence_name 32 | 33 | 34 | 35 | // End of these definitions 36 | -------------------------------------------------------------------------------- /wquery/SCRIPT:operon.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2006-02-15_17:16:50 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Operon 18 | From 1 19 | Condition CEOP192 20 | 21 | Colonne 2 22 | Width 30 23 | Mandatory 24 | Visible 25 | Class 26 | Class Gene 27 | From 1 28 | Tag Contains_gene 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/allele_designation_to_LAB.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-28_13:27:59 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Laboratory 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Text 25 | From 1 26 | Tag Allele_designation 27 | 28 | 29 | 30 | // End of these definitions 31 | -------------------------------------------------------------------------------- /wquery/allele_has_seq.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-02-11_10:35:56 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Variation 18 | From 1 19 | Condition Sequence 20 | 21 | Colonne 2 22 | Width 12 23 | Optional 24 | Visible 25 | Class 26 | Class Sequence 27 | From 1 28 | Tag Sequence 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/allele_to_gene_id.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-02-11_10:36:16 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Variation 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Gene 26 | From 1 27 | Tag Gene 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/allele_to_locus.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-02-11_10:35:07 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title Variations with allele, gene 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Width 12 16 | Optional 17 | Visible 18 | Class 19 | Class Variation 20 | From 1 21 | 22 | Colonne 2 23 | Width 20 24 | Mandatory 25 | Visible 26 | Class 27 | Class Gene 28 | From 1 29 | Tag Gene 30 | 31 | Colonne 3 32 | Width 12 33 | Mandatory 34 | Hidden 35 | Show_Tag 36 | Right_of 1 37 | Tag Allele 38 | 39 | 40 | 41 | // End of these definitions 42 | -------------------------------------------------------------------------------- /wquery/cDNA2CDS.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-01-30_16:47:22 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title cDNA names to latest ORF names 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle cDNA name 16 | Width 20 17 | Optional 18 | Visible 19 | Class 20 | Class cDNA_Sequence 21 | From 1 22 | 23 | Colonne 2 24 | Subtitle Corresponding ORF 25 | Width 20 26 | Mandatory 27 | Visible 28 | Class 29 | Class CDS 30 | From 1 31 | Tag Matching_CDS 32 | 33 | 34 | 35 | // End of these definitions 36 | -------------------------------------------------------------------------------- /wquery/cDNApairs.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: ar2 3 | // Date: 2003-11-20_14:49:49 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class cDNA_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Sequence 26 | From 1 27 | Tag Paired_read 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/cds2lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-04-21_11:40:58 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class elegans_CDS 18 | From 1 19 | Condition * 20 | 21 | Colonne 2 22 | Width 12 23 | Optional 24 | Visible 25 | Class 26 | Class Laboratory 27 | From 1 28 | Tag From_laboratory 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/cds_est.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: ah3 3 | // Date: 2002-07-29_15:10:35 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Predicted_gene 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Sequence 26 | From 1 27 | Tag Matching_cDNA 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/cgc2cds.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-02-22_13:55:11 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 20 14 | Optional 15 | Visible 16 | Class 17 | Class Gene 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Gene_name 26 | From 1 27 | Tag CGC_name 28 | 29 | Colonne 3 30 | Width 12 31 | Optional 32 | Visible 33 | Class 34 | Class CDS 35 | From 1 36 | Tag Corresponding_CDS 37 | 38 | 39 | 40 | // End of these definitions 41 | -------------------------------------------------------------------------------- /wquery/clone2map.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2001-09-08_15:36:51 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Genome_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Map 26 | From 1 27 | Tag Map 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/clone2type.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-05-19_14:35:51 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Clone 18 | From 1 19 | Condition Sequence 20 | 21 | Colonne 2 22 | Width 12 23 | Mandatory 24 | Visible 25 | Next_Tag 26 | From 1 27 | Tag Type 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/clone_to_lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-01-05_13:18:57 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Genome_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Laboratory 26 | From 1 27 | Tag From_Laboratory 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/clonesize.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-03-03_13:11:13 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Genome_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Hidden 24 | Class 25 | Class DNA 26 | From 1 27 | Tag DNA 28 | 29 | Colonne 3 30 | Width 12 31 | Optional 32 | Visible 33 | Integer 34 | Right_of 2 35 | Tag HERE 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/col_cosmid.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: dl1 3 | // Date: 1995-11-29_16:07:45 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // \%n (%n in the graphic) are substituted by the value of column n at run time 7 | // Line starting with // are ignored, starting with # are comments 8 | 9 | Colonne 1 10 | Width 12 11 | Mandatory 12 | Visible 13 | Class 14 | Class Sequence 15 | From 0 16 | 17 | Colonne 2 18 | Width 12 19 | Mandatory 20 | Hidden 21 | Class 22 | Class Text 23 | From 1 24 | Tag Brief_identification 25 | Condition collagen 26 | 27 | Colonne 3 28 | Width 12 29 | Optional 30 | Visible 31 | Class 32 | Class Sequence 33 | From 1 34 | Tag Matching_cDNA 35 | 36 | 37 | 38 | // End of these definitions 39 | -------------------------------------------------------------------------------- /wquery/deleted_ESTs.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2002-10-22_15:49:18 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Sequence 26 | From 1 27 | Tag Matching_Genomic 28 | 29 | Colonne 3 30 | Width 32 31 | Optional 32 | Visible 33 | Class 34 | Class Homol_data 35 | From 1 36 | Tag Homol_homol 37 | 38 | 39 | 40 | // End of these definitions 41 | -------------------------------------------------------------------------------- /wquery/dl-960813.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // Date: 1996-08-13_10:28:55 3 | 4 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 5 | // \%n (%n in the graphic) are substituted by the value of column n at run time 6 | // Line starting with // are ignored, starting with # are comments 7 | 8 | Colonne 1 9 | Width 12 10 | Optional 11 | Visible 12 | Class 13 | Class Genome_Sequence 14 | From 0 15 | 16 | Colonne 2 17 | Width 12 18 | Mandatory 19 | Visible 20 | Date 21 | From 1 22 | Tag Finished 23 | 24 | Colonne 3 25 | Width 12 26 | Mandatory 27 | Visible 28 | Class 29 | Class Map 30 | From 1 31 | Tag Map 32 | 33 | Colonne 4 34 | Width 12 35 | Optional 36 | Visible 37 | Float 38 | Right_of 3 39 | 40 | 41 | 42 | // End of these definitions 43 | -------------------------------------------------------------------------------- /wquery/external.parameter.def: -------------------------------------------------------------------------------- 1 | // @(#)external.parameter.def 1.1 8/8/95 2 | // Spread sheet definition for the ACeDB software 3 | // User: mieg 4 | // Date: 94-11-22_20:19:37 5 | 6 | // Line starting with // are ignored, starting with # are comments 7 | 8 | Colonne 1 9 | Width 12 10 | Optional 11 | Visible 12 | Class 13 | Class Author 14 | From 0 15 | Condition IS %1 16 | 17 | 18 | 19 | // End of these definitions 20 | -------------------------------------------------------------------------------- /wquery/geneace/CGC_table-3_intmap.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-11-10_17:16:26 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Locus 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Map 26 | From 1 27 | Tag Interpolated_map_position 28 | 29 | Colonne 3 30 | Width 12 31 | Optional 32 | Visible 33 | Float 34 | Right_of 2 35 | Tag HERE 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/geneace/CGC_table-3_map.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-11-10_17:14:37 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Locus 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Map 26 | From 1 27 | Tag Map 28 | 29 | Colonne 3 30 | Width 12 31 | Optional 32 | Visible 33 | Float 34 | Right_of 2 35 | Tag HERE # Position 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/2-pt.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-08-18_12:24:31 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class 2_point_data 18 | From 1 19 | 20 | 21 | 22 | // End of these definitions 23 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/KO_allele_flank_seqs.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-09-26_14:39:26 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class KO_allele 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Text 25 | From 1 26 | Tag Flanking_sequences 27 | 28 | Colonne 3 29 | Width 12 30 | Mandatory 31 | Visible 32 | Text 33 | Right_of 2 34 | Tag HERE 35 | 36 | 37 | 38 | // End of these definitions 39 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/WBPerson_not_linked_to_lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-21_13:33:20 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | 11 | Colonne 1 12 | Width 12 13 | Optional 14 | Visible 15 | Class 16 | Class Person 17 | From 1 18 | 19 | Colonne 2 20 | Width 21 | Null 22 | Visible 23 | Class 24 | Class Person 25 | From 1 26 | Tag Laboratory 27 | 28 | // End of these definitions 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/allele_has_flankSeq_and_no_seq.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-16_16:19:30 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Allele 18 | From 1 19 | Condition flanking_sequences 20 | 21 | Colonne 2 22 | Width 12 23 | Null 24 | Visible 25 | Class 26 | Class Sequence 27 | From 1 28 | Tag Sequence 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/allele_method_has_no_isolation_tag.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-02-26_11:49:51 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Allele 18 | From 1 19 | Condition Method = "Knockout_allele" | Method = "Transposon_insertion" 20 | 21 | Colonne 2 22 | Width 12 23 | Null 24 | Visible 25 | Show_Tag 26 | From 1 27 | Tag Isolation 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/allele_methods.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-02-26_10:45:33 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Allele 18 | From 1 19 | Condition !Method 20 | 21 | Colonne 2 22 | Width 12 23 | Optional 24 | Visible 25 | Show_Tag 26 | From 1 27 | Tag Transposon_insertion 28 | 29 | Colonne 3 30 | Width 12 31 | Optional 32 | Visible 33 | Show_Tag 34 | From 1 35 | Tag KO_consortium_allele 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/cgc_approved_loci.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: ck1 3 | // Date: 2003-02-14_10:23:16 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Locus 18 | From 1 19 | Condition cgc_approved 20 | 21 | 22 | 23 | // End of these definitions 24 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/lab_representative.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-07-28_11:58:54 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Laboratory 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Person 26 | From 1 27 | Tag Representative 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/laboratory_has_person.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-21_13:33:20 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Laboratory 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Person 26 | From 1 27 | Tag Person 28 | 29 | 30 | // End of these definitions 31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/loci_not_linked_to_seq.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-07-16_15:57:25 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Locus 18 | From 1 19 | Condition !(CDS | transcript) 20 | 21 | 22 | 23 | // End of these definitions 24 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/locus_data.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: ar2 3 | // Date: 2002-06-11_13:39:59 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title locus 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Width 12 16 | Mandatory 17 | Visible 18 | Class 19 | Class Locus 20 | From 1 21 | 22 | Colonne 2 23 | Width 12 24 | optional 25 | Visible 26 | Class 27 | Class Sequence 28 | From 1 29 | Tag CDS 30 | 31 | Colonne 3 32 | Width 12 33 | optional 34 | visible 35 | Show_Tag 36 | From 1 37 | Tag Other_name 38 | 39 | 40 | 41 | // End of these definitions 42 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/locus_has_genomic_seq.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-21_13:33:20 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Locus 18 | From 1 19 | Condition CDS 20 | 21 | 22 | 23 | // End of these definitions 24 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/locus_in_strain.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-06-06_15:03:57 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Strain 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Locus 26 | From 1 27 | Tag Gene 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/locus_pseudogene.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-28_10:40:20 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title Locus->Pseudogene 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle Locus 16 | Width 12 17 | Optional 18 | Visible 19 | Class 20 | Class Locus 21 | From 1 22 | Condition CGC_approved 23 | 24 | Colonne 2 25 | Subtitle Pseudogene 26 | Width 12 27 | Mandatory 28 | Visible 29 | Class 30 | Class Pseudogene 31 | From 1 32 | Tag Pseudogene 33 | 34 | 35 | 36 | // End of these definitions 37 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/locus_seq.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-28_10:40:53 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title Locus->Sequence connections 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle Locus 16 | Width 12 17 | Optional 18 | Visible 19 | Class 20 | Class Locus 21 | From 1 22 | Condition CGC_approved 23 | 24 | Colonne 2 25 | Subtitle Sequence 26 | Width 12 27 | Mandatory 28 | Visible 29 | Class 30 | Class CDS 31 | From 1 32 | Tag CDS 33 | 34 | 35 | 36 | // End of these definitions 37 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/locus_to_Transcripts.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-06-05_12:26:37 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Locus 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Transcript 26 | From 1 27 | Tag Transcript 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/locus_transcript.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-28_10:40:20 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title Locus->Transcript 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle Locus 16 | Width 12 17 | Optional 18 | Visible 19 | Class 20 | Class Locus 21 | From 1 22 | Condition CGC_approved 23 | 24 | Colonne 2 25 | Subtitle Transcript 26 | Width 12 27 | Mandatory 28 | Visible 29 | Class 30 | Class Transcript 31 | From 1 32 | Tag Transcript 33 | 34 | 35 | 36 | // End of these definitions 37 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/multi-pt.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-08-18_12:24:09 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Multi_pt_data 18 | From 1 19 | 20 | 21 | 22 | // End of these definitions 23 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/person_also_known_as.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-05-20_15:58:01 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Person 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Person_name 26 | From 1 27 | Tag Also_known_as 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/geneace/REMOVED/pos-neg.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-08-18_12:24:45 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Pos_neg_data 18 | From 1 19 | 20 | 21 | 22 | // End of these definitions 23 | -------------------------------------------------------------------------------- /wquery/geneace/SCRIPT:GeneID_updater.pl.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-05-09_13:36:18 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title WBGeneID check 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle Gene 16 | Width 20 17 | Optional 18 | Visible 19 | Class 20 | Class Gene 21 | From 1 22 | 23 | Colonne 2 24 | Subtitle Seq_name 25 | Width 18 26 | Optional 27 | Visible 28 | Class 29 | Class Gene_name 30 | From 1 31 | Tag Sequence_name 32 | 33 | 34 | 35 | // End of these definitions 36 | -------------------------------------------------------------------------------- /wquery/geneace/SCRIPT:operon.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2006-02-15_17:16:50 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Operon 18 | From 1 19 | Condition CEOP192 20 | 21 | Colonne 2 22 | Width 30 23 | Mandatory 24 | Visible 25 | Class 26 | Class Gene 27 | From 1 28 | Tag Contains_gene 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/geneace/allele_designation_to_LAB.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-01-28_13:27:59 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Laboratory 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Text 25 | From 1 26 | Tag Allele_designation 27 | 28 | 29 | 30 | // End of these definitions 31 | -------------------------------------------------------------------------------- /wquery/geneace/allele_has_seq.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-02-11_10:35:56 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Variation 18 | From 1 19 | Condition Sequence 20 | 21 | Colonne 2 22 | Width 12 23 | Optional 24 | Visible 25 | Class 26 | Class Sequence 27 | From 1 28 | Tag Sequence 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/geneace/allele_to_gene_id.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2005-02-11_10:36:16 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Variation 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Gene 26 | From 1 27 | Tag Gene 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/geneace/clone_to_lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-01-05_13:18:57 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Genome_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Laboratory 26 | From 1 27 | Tag From_Laboratory 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/geneace/genome_seq_to_lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: ck1 3 | // Date: 2003-08-21_17:03:00 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Subtitle allele objects 14 | Width 12 15 | Optional 16 | Visible 17 | Class 18 | Class Genome_Sequence 19 | From 1 20 | Condition * 21 | 22 | Colonne 2 23 | Width 12 24 | Mandatory 25 | Visible 26 | Class 27 | Class Laboratory 28 | From 1 29 | Tag From_Laboratory 30 | 31 | 32 | 33 | // End of these definitions 34 | -------------------------------------------------------------------------------- /wquery/geneace/get_WBPersonID_fn_ln.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-06-09_16:26:29 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Person 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Text 25 | From 1 26 | Tag First_name 27 | 28 | Colonne 3 29 | Width 12 30 | Optional 31 | Visible 32 | Class 33 | Class Person_name 34 | From 1 35 | Tag Last_name 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/geneace/get_elegans_CDS_source_exons.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: ck1 3 | // Date: 2004-01-06_16:33:24 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class elegans_CDS 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Integer 25 | Right_of 1 26 | Tag Source_Exons 27 | 28 | Colonne 3 29 | Width 12 30 | Optional 31 | Visible 32 | Integer 33 | Right_of 2 34 | Tag HERE 35 | 36 | 37 | 38 | // End of these definitions 39 | -------------------------------------------------------------------------------- /wquery/geneace/get_elegans_RNA_gene_source_exons.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: ck1 3 | // Date: 2004-01-06_16:35:12 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class elegans_RNA_genes 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Integer 25 | Right_of 1 26 | Tag Source_Exons 27 | 28 | Colonne 3 29 | Width 12 30 | Optional 31 | Visible 32 | Integer 33 | Right_of 2 34 | Tag HERE 35 | 36 | 37 | 38 | // End of these definitions 39 | -------------------------------------------------------------------------------- /wquery/geneace/locus_2_gmap.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-03-11_17:14:19 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Locus 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Map 26 | From 1 27 | Tag Map 28 | 29 | Colonne 3 30 | Width 12 31 | Mandatory 32 | Visible 33 | Float 34 | Right_of 2 35 | Tag HERE # Position 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/geneace/strain_genotype.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-07-21_14:23:49 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Strain 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Text 25 | From 1 26 | Tag Genotype 27 | 28 | 29 | 30 | // End of these definitions 31 | -------------------------------------------------------------------------------- /wquery/geneace/transgene_ids.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: klh 3 | // Date: 2013-02-02_09:52:29 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Transgene 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Class 25 | Class Text 26 | From 1 27 | Tag Public_name 28 | 29 | 30 | 31 | // End of these definitions 32 | -------------------------------------------------------------------------------- /wquery/geneace/variation_nameserver_comm.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2010-11-26_11:08:57 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Variation 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Next_Tag 25 | From 1 26 | Tag Status 27 | 28 | Colonne 3 29 | Width 12 30 | Optional 31 | Visible 32 | Class 33 | Class Variation_name 34 | From 1 35 | Tag Public_name 36 | 37 | 38 | // End of these definitions 39 | -------------------------------------------------------------------------------- /wquery/genelist.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-03-03_15:48:39 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class CDS 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Locus 26 | From 1 27 | Tag Locus 28 | 29 | Colonne 3 30 | Width 52 31 | Optional 32 | Visible 33 | Class 34 | Class Text 35 | From 1 36 | Tag Brief_identification 37 | 38 | 39 | 40 | // End of these definitions 41 | -------------------------------------------------------------------------------- /wquery/get_CDS_to_gene.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-04-19_10:38:35 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Subtitle predicted_gene names 14 | Width 12 15 | Optional 16 | Visible 17 | Class 18 | Class CDS 19 | From 1 20 | Condition Gene 21 | 22 | Colonne 2 23 | Width 12 24 | Mandatory 25 | Visible 26 | Class 27 | Class Gene 28 | From 1 29 | Tag Gene 30 | 31 | 32 | 33 | // End of these definitions 34 | -------------------------------------------------------------------------------- /wquery/get_WBPersonID_fn_ln.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-06-09_16:26:29 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Person 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Text 25 | From 1 26 | Tag First_name 27 | 28 | Colonne 3 29 | Width 12 30 | Optional 31 | Visible 32 | Class 33 | Class Person_name 34 | From 1 35 | Tag Last_name 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/get_predicted_gene_to_locus.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-12-15_10:43:05 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Subtitle predicted_gene names 14 | Width 12 15 | Optional 16 | Visible 17 | Class 18 | Class CDS 19 | From 1 20 | Condition Locus 21 | 22 | Colonne 2 23 | Width 12 24 | Mandatory 25 | Visible 26 | Class 27 | Class Locus 28 | From 1 29 | Tag Locus 30 | 31 | 32 | 33 | // End of these definitions 34 | -------------------------------------------------------------------------------- /wquery/get_pseudogene_to_gene.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-04-19_10:42:27 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Subtitle predicted_gene names 14 | Width 12 15 | Optional 16 | Visible 17 | Class 18 | Class Pseudogene 19 | From 1 20 | Condition Gene 21 | 22 | Colonne 2 23 | Width 12 24 | Mandatory 25 | Visible 26 | Class 27 | Class Gene 28 | From 1 29 | Tag Gene 30 | 31 | 32 | 33 | // End of these definitions 34 | -------------------------------------------------------------------------------- /wquery/get_transcript_to_gene.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-04-19_10:40:48 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Subtitle predicted_gene names 14 | Width 12 15 | Optional 16 | Visible 17 | Class 18 | Class Transcript 19 | From 1 20 | Condition Gene 21 | 22 | Colonne 2 23 | Width 12 24 | Mandatory 25 | Visible 26 | Class 27 | Class Gene 28 | From 1 29 | Tag Gene 30 | 31 | 32 | 33 | // End of these definitions 34 | -------------------------------------------------------------------------------- /wquery/id2clone.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2001-09-06_16:11:35 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Genome_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Hidden 24 | Class 25 | Class Database 26 | From 1 27 | Tag Database 28 | 29 | Colonne 3 30 | Width 12 31 | Mandatory 32 | Visible 33 | Class 34 | Class Text 35 | Right_of 2 36 | Tag HERE 37 | 38 | 39 | 40 | // End of these definitions 41 | -------------------------------------------------------------------------------- /wquery/journal.def: -------------------------------------------------------------------------------- 1 | // @(#)journal.def 1.1 8/8/95 2 | // Spread sheet definition for the ACeDB software 3 | // User: mieg 4 | // Date: 95-03-07_13:30:03 5 | 6 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Colonne 1 11 | Width 12 12 | Mandatory 13 | Visible 14 | Class 15 | Class Journal 16 | From 0 17 | Tag "(null)" 18 | Condition "n*" 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Paper 26 | From 1 27 | Tag Paper 28 | 29 | Colonne 3 30 | Width 12 31 | Mandatory 32 | Visible 33 | Integer 34 | From 2 35 | Tag Year 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/methods.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2001-10-22_13:21:53 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 3 11 | 12 | Colonne 1 13 | Width 30 14 | Optional 15 | Visible 16 | Class 17 | Class Method 18 | From 1 19 | 20 | Colonne 2 21 | Width 20 22 | Optional 23 | Visible 24 | Next_Tag 25 | From 1 26 | Tag Colour 27 | 28 | Colonne 3 29 | Width 12 30 | Mandatory 31 | Visible 32 | Float 33 | Right_of 2 34 | Tag Right_priority 35 | 36 | 37 | 38 | // End of these definitions 39 | -------------------------------------------------------------------------------- /wquery/new_sequences.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2001-04-24_09:49:56 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 2 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Genome_Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Visible 24 | Date 25 | From 1 26 | Tag Date 27 | 28 | 29 | 30 | // End of these definitions 31 | -------------------------------------------------------------------------------- /wquery/problem_S_children.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2002-03-04_16:57:24 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 25 22 | Mandatory 23 | Visible 24 | Class 25 | Class PCR_product 26 | From 1 27 | Tag PCR_product 28 | 29 | Colonne 3 30 | Width 12 31 | Mandatory 32 | Visible 33 | Class ... 34 | Count 35 | Right_of 2 36 | Tag HERE 37 | Condition !1 38 | 39 | 40 | 41 | // End of these definitions 42 | -------------------------------------------------------------------------------- /wquery/pseudogene2lab.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-04-21_11:39:28 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class elegans_pseudogenes 18 | From 1 19 | Condition * 20 | 21 | Colonne 2 22 | Width 12 23 | Optional 24 | Visible 25 | Class 26 | Class Laboratory 27 | From 1 28 | Tag From_laboratory 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/strain_genotype.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2003-07-21_14:23:49 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Strain 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Text 25 | From 1 26 | Tag Genotype 27 | 28 | 29 | 30 | // End of these definitions 31 | -------------------------------------------------------------------------------- /wquery/tRNA_info_1.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2001-03-09_11:55:42 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Sequence 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Optional 23 | Visible 24 | Class 25 | Class Sequence 26 | From 1 27 | Tag Source 28 | 29 | Colonne 3 30 | Width 12 31 | Optional 32 | Visible 33 | Text 34 | From 1 35 | Tag tRNA 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/using.author.def: -------------------------------------------------------------------------------- 1 | // @(#)using.author.def 1.1 8/8/95 2 | 3 | @wquery/author.paper.def *mieg* 4 | -------------------------------------------------------------------------------- /wquery/wormpep2.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2001-01-17_18:11:42 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Sequence 18 | From 1 19 | Condition Genomic_canonical OR *LINK* 20 | 21 | Colonne 2 22 | Width 12 23 | Mandatory 24 | Visible 25 | Class 26 | Class Laboratory 27 | From 1 28 | Tag From_Laboratory 29 | 30 | 31 | 32 | // End of these definitions 33 | -------------------------------------------------------------------------------- /wquery/wormpep_lengths.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: ar2 3 | // Date: 2004-07-02_10:25:23 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Sortcolumn 1 11 | 12 | Colonne 1 13 | Width 12 14 | Optional 15 | Visible 16 | Class 17 | Class Wormpep 18 | From 1 19 | 20 | Colonne 2 21 | Width 12 22 | Mandatory 23 | Hidden 24 | Class 25 | Class Peptide 26 | From 1 27 | Tag Peptide 28 | 29 | Colonne 3 30 | Width 12 31 | Mandatory 32 | Visible 33 | Integer 34 | Right_of 2 35 | Tag HERE 36 | 37 | 38 | 39 | // End of these definitions 40 | -------------------------------------------------------------------------------- /wquery/yk2ORF.def: -------------------------------------------------------------------------------- 1 | // Spread sheet definition for the ACeDB software 2 | // User: wormpub 3 | // Date: 2004-01-30_16:47:22 4 | 5 | // %n (%%n in the graphic) are parameter to be given on the command line in tace 6 | // or by default by the Parameters given in this file 7 | // \%n (%n in the graphic) are substituted by the value of column n at run time 8 | // Line starting with // are ignored, starting with # are comments 9 | 10 | Title yk names to latest ORF names 11 | 12 | Sortcolumn 1 13 | 14 | Colonne 1 15 | Subtitle yk EST name 16 | Width 20 17 | Optional 18 | Visible 19 | Class 20 | Class cDNA_Sequence 21 | From 1 22 | Condition yk* 23 | 24 | Colonne 2 25 | Subtitle Corresponding ORF 26 | Width 20 27 | Mandatory 28 | Visible 29 | Class 30 | Class CDS 31 | From 1 32 | Tag Matching_CDS 33 | 34 | 35 | 36 | // End of these definitions 37 | -------------------------------------------------------------------------------- /wspec/constraints.wrm: -------------------------------------------------------------------------------- 1 | // constraints.wrm 2 | // @(#)constraints.wrm 1.1 4/15/97 3 | 4 | // A constraint given on a class will be checked 5 | // before saving an object while parsing an ace file 6 | // if an object does not satisfy the constraint, 7 | // you will get a parse error 8 | 9 | // Example 10 | 11 | // Class Paper 12 | // Constraints "Year:1" 13 | 14 | // this will imply that you cannot edit a paper 15 | // that does not have a Year value, 16 | // i.e. field 1 right of Year must be non void 17 | 18 | // any acedb query LOCAL to a single object is valid 19 | // don t use: FIND or FOLLOW constructions 20 | 21 | -------------------------------------------------------------------------------- /wspec/copyright: -------------------------------------------------------------------------------- 1 | /* Copyright (C) 1991-1998 R Durbin and J Thierry-Mieg. 2 | * All rights reserved. 3 | * Written by Jean Thierry-Mieg and Richard Durbin, 1990-1998, with 4 | * assistance and code from others as indicated at the head of source 5 | * code modules. 6 | * Redistribution and use in source and binary forms are freely 7 | * permitted provided that the above copyright notice and 8 | * attribution and date of work and this paragraph are duplicated 9 | * in all such forms and that neither this software nor software 10 | * based in whole or in part on this software is sold for profit. 11 | * THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR 12 | * IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED 13 | * WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR 14 | * PURPOSE. 15 | */ 16 | 17 | /* $Id: copyright,v 1.1 2001-06-08 10:53:28 jws Exp $ */ 18 | --------------------------------------------------------------------------------