├── .gitattributes ├── .gitignore ├── .idea ├── .name ├── Proteoformer.iml ├── encodings.xml ├── misc.xml ├── modules.xml ├── vcs.xml └── workspace.xml ├── 1_mapping ├── mapping.pl ├── mapping.xml ├── mapping_parsing.pl └── mapping_plastid.pl ├── 1_mapping_py3 ├── mapping.pl ├── mapping.xml ├── mapping_parsing.pl └── mapping_plastid.pl ├── 2_mappingQC ├── README_mappingqc.txt ├── mappingQC.pl ├── mappingQC.xml └── mqc_tools │ ├── install_pyplot3D_mod.py │ ├── mappingQC.py │ ├── metagenic_piecharts.R │ ├── quality_plots.R │ ├── simulate_utr_for_prokaryotes.py │ └── site-packages │ └── axes3d.py ├── 2_mappingQC_py3 ├── README_mappingqc.txt ├── mappingQC.pl ├── mappingQC.xml └── mqc_tools │ ├── mappingQC.py │ ├── metagenic_piecharts.R │ ├── quality_plots.R │ ├── simulate_utr_for_prokaryotes.py │ └── site-packages │ └── axes3d.py ├── 3_tr_calling ├── Galaxy_files │ ├── transcript_calling.pl │ └── transcript_calling.xml ├── RiboZINB │ └── RiboZINB.py ├── Rule-based │ └── ribo_translation.pl └── from_RNA │ ├── parse_transcripts_featurecounts.py │ └── parse_transcripts_salmon.py ├── 4_ORF_calling ├── from_RNA │ └── based_on_Salmon_output │ │ └── RNA_ORF_assembly.py ├── using_PRICE │ ├── PRICE.py │ └── Price_1.0.2 │ │ ├── gedi │ │ ├── gedi.jar │ │ ├── lib │ │ ├── BigWig.jar │ │ ├── R.jar │ │ ├── ant.jar │ │ ├── asm-4.2.jar │ │ ├── asm-commons-4.2.jar │ │ ├── asm-util-4.2.jar │ │ ├── colt.jar │ │ ├── commons-cli-1.2.jar │ │ ├── commons-compress-1.5.jar │ │ ├── commons-math3-3.4.1.jar │ │ ├── concurrent.jar │ │ ├── controlsfx-8.40.12.jar │ │ ├── fern.jar │ │ ├── fontawesomefx-8.0.13.jar │ │ ├── freehep-graphics2d.jar │ │ ├── freehep-psviewer.jar │ │ ├── fst-2.43.jar │ │ ├── h2-1.4.177.jar │ │ ├── hamcrest-all-1.3.jar │ │ ├── htsjdk-2.2.1.jar │ │ ├── j2html-1.0.0.jar │ │ ├── jackson-core-2.5.3.jar │ │ ├── jansi.jar │ │ ├── javax.json-1.0.4.jar │ │ ├── javax.servlet-api-3.1.0.jar │ │ ├── jdistlib-0.4.4-bin.jar │ │ ├── jdom.jar │ │ ├── jericho-html-3.4.jar │ │ ├── jetty-client-9.4.6.v20170531.jar │ │ ├── jetty-http-9.4.6.v20170531.jar │ │ ├── jetty-io-9.4.6.v20170531.jar │ │ ├── jetty-security-9.4.6.v20170531.jar │ │ ├── jetty-server-9.4.6.v20170531.jar │ │ ├── jetty-servlet-9.4.6.v20170531.jar │ │ ├── jetty-util-9.4.6.v20170531.jar │ │ ├── jetty-webapp-9.4.6.v20170531.jar │ │ ├── jetty-xml-9.4.6.v20170531.jar │ │ ├── jlatexmath-1.0.4.jar │ │ ├── json-20160810.jar │ │ ├── jtar-2.3.jar │ │ ├── junit-4.11.jar │ │ ├── junit-benchmarks-0.7.2.jar │ │ ├── junit.jar │ │ ├── jzlib-1.1.3.jar │ │ ├── libsvm.jar │ │ ├── log4j-1.2.15.jar │ │ ├── lz4-1.3-SNAPSHOT.jar │ │ ├── mysql-connector-java-5.1.30-bin.jar │ │ ├── netty-all-4.1.0.Beta3.jar │ │ ├── objenesis-2.1.jar │ │ ├── slf4j-api-1.7.21.jar │ │ ├── slf4j-simple-1.7.21.jar │ │ ├── smile-core-1.3.1.jar │ │ ├── smile-data-1.3.1.jar │ │ ├── smile-graph-1.3.1.jar │ │ ├── smile-math-1.3.1.jar │ │ ├── spark-core-2.6.0.jar │ │ ├── sra_xml.jar │ │ ├── websocket-api-9.4.6.v20170531.jar │ │ ├── websocket-client-9.4.6.v20170531.jar │ │ ├── websocket-common-9.4.6.v20170531.jar │ │ ├── websocket-server-9.4.6.v20170531.jar │ │ └── websocket-servlet-9.4.6.v20170531.jar │ │ ├── output.clusters.csv │ │ ├── output.maxPos │ │ ├── output.param │ │ └── reads.bamlist ├── using_SPECtre │ ├── SPECtre.py │ └── tmp │ │ └── SPECtre │ │ └── spectre-master │ │ ├── README.md │ │ ├── SPECtre.py │ │ ├── SPECtre.pyc │ │ ├── __init__.py │ │ ├── scripts │ │ ├── __init__.py │ │ ├── calculate_psite_offsets.py │ │ ├── map_ensembl_to_ucsc.py │ │ └── merge_split_spectre_files.py │ │ └── test │ │ ├── Homo_sapiens.GRCh38.78.test.gtf │ │ ├── isoforms-test.fpkm_tracking │ │ ├── spectre_test.log │ │ ├── spectre_test.txt │ │ ├── test.bam │ │ └── test.bam.bai └── using_treated_TIS_calling │ ├── 4a_tis_calling │ ├── TIScalling_categorised.pl │ └── tis_calling.xml │ ├── 4b_variation_calling │ └── SNPanalysis │ │ ├── READMEsnpcalling.txt │ │ ├── snp_calling │ │ ├── snp_calling.xml │ │ └── tools │ │ ├── filterSAMfile.pl │ │ ├── snpIndexBuilder.pl │ │ └── splitVCFaltRecords.pl │ └── 4c_translation_assembly │ ├── assembly.pl │ └── assembly.xml ├── 5_tis_overview ├── TIS_overview.pl └── tis_overview.xml ├── 6_orf_based_counts └── ORFbasedCounts.py ├── 7_translation_database ├── deduplicate_fasta.py ├── filter_uncanonical_AAs.py ├── generate_translation_db.pl ├── generate_translation_db.xml └── split_fasta.py ├── 8_floss_calculation ├── FlossProteoformer.pl └── FlossProteoformer.xml ├── 9_summarize_feature └── summarize_feature.py ├── Additional_tools ├── ENS_db.py ├── ENS_db_py3.py ├── MaxQuant_results_parsing │ ├── parse_maxquant.py │ ├── parse_maxquant_uniprot.py │ ├── parse_maxquant_uniprot_rnaseq.py │ └── protein_inference │ │ ├── analyse_proteoforms.py │ │ └── analyse_proteoforms_rnaseq.py ├── Percolator_results_parsing │ ├── old_scripts │ │ ├── include_decoy_and_contaminants.py │ │ └── parse_percolator_PI.py │ ├── post_processing_tools.py │ └── protein_inference │ │ ├── ribo │ │ ├── analyse_proteoforms_percolator.py │ │ ├── classify_proteoforms_percolator.py │ │ ├── compare_mq_percolator.py │ │ ├── include_decoy_and_contaminants.py │ │ └── rearrange_prosit_tab.py │ │ └── rna │ │ ├── analyse_proteoforms_percolator_rnaseq.py │ │ ├── compare_mq_percolator_rnaseq.py │ │ └── rearrange_ms2rescore_tab.py ├── download_sra_parallel.sh ├── fasta_combination │ ├── different_TIS_ids │ │ ├── combfasta2sqlite.py │ │ └── combine_dbs.py │ ├── with_hspvdb │ │ ├── combine_with_hspvdb.py │ │ └── convert_hspvdb.py │ └── with_uniprot │ │ ├── cne_canonicalfasta_converter.py │ │ ├── combine_with_uniprot.py │ │ ├── combine_with_uniprot_py3.py │ │ └── combuniprot2sqlite.py ├── get_igenomes.py ├── get_igenomes_py3.py ├── normBedgraph └── simulate_utr_for_prokaryotes.py ├── Dependency_envs ├── download_sra_parallel.yml ├── old_ymls │ ├── install_add_perl_tools.pl │ ├── proteoformer_py2.yml │ └── proteoformer_py3.yml ├── price.yml ├── proteoformer_general.yml ├── proteoformer_multiqc.yml ├── proteoformer_plastid.yml ├── ribozinb.yml └── spectre.yml ├── Galaxy files ├── loc files │ ├── ENS_db.loc │ ├── blast_db.loc │ ├── blastp_db.loc │ ├── igenomes.loc │ ├── snpdb.loc │ └── ublast_db.loc ├── tool_conf.xml └── tool_data_table_conf.xml ├── LICENSE ├── LogoBanner ├── Banner_proteoformer20.jpg ├── ohmx_logo01_2.svg └── proteoformerLogo.jpg ├── README.md ├── examples_commands.md ├── proteoformer_pipeline_py2.sh └── proteoformer_pipeline_py3.sh /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Biobix/proteoformer/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Biobix/proteoformer/HEAD/.gitignore -------------------------------------------------------------------------------- /.idea/.name: 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