├── .gitignore ├── LICENSE ├── README.md ├── about.php ├── annot_desc.php ├── annot_desc_file.php ├── cookies.php ├── css ├── bootstrap.min.css ├── datatables.css ├── datatables.min.css ├── datatables │ ├── buttons.bootstrap4.min.css │ ├── colReorder.dataTables.min.css │ ├── dataTables.bootstrap4.min.css │ └── datatables.min.css ├── easy_gdb.css └── loading_datatable.css ├── custom_view.php ├── downloads.php ├── favicon.ico ├── footer.php ├── gene.php ├── gene_seq.php ├── groups.php ├── header.php ├── help ├── 00_help.php ├── 01_search.php ├── 02_blast.php ├── 03_genome_browser.php ├── 04_sequence_extraction.php ├── 05_annotation_extraction.php ├── 06_gene_lookup.php ├── 07_gene_enrichment.php ├── 08_gene_expression.php ├── 09_expression_comparator.php ├── 10_coexpression.php ├── header_help.php └── help_images │ ├── JBrowse_cookies.png │ ├── JBrowse_example.png │ ├── annotation_extraction.png │ ├── annotext_example.png │ ├── average.png │ ├── blast.png │ ├── blast_options.png │ ├── blast_result.png │ ├── cards.png │ ├── coex_input.png │ ├── coex_output.png │ ├── gene_expression.png │ ├── gene_lookup.png │ ├── gene_lookup_example1.png │ ├── heatmap.png │ ├── heatmap_example.png │ ├── heatmap_highligh_1.png │ ├── heatmap_highligh_2.png │ ├── input.png │ ├── input_comparator.png │ ├── input_enrichment.png │ ├── input_lookup.png │ ├── lines.png │ ├── lines_comparator.png │ ├── lines_comparator_1.png │ ├── lines_comparator_2.png │ ├── lines_comparator_highlight.png │ ├── lines_comparator_highlight_1.png │ ├── lines_comparator_highlight_2.png │ ├── lines_example.png │ ├── lines_hide.png │ ├── lines_highlight.png │ ├── output_enrichment.png │ ├── output_enrichment_1.png │ ├── output_enrichment_2.png │ ├── replicates.png │ ├── search-example1.png │ ├── search_example.png │ ├── search_example_output.png │ ├── search_mainpage.png │ └── sequence_extraction.png ├── index.php ├── install ├── Dockerfile ├── docker-compose.yml ├── easy_gdb_apache.conf └── setup.sh ├── jb_frame.php ├── jb_frame_file.php ├── js ├── Datatables │ ├── buttons.bootstrap4.min.js │ ├── buttons.colVis.min.js │ ├── buttons.html5.min.js │ ├── buttons.print.min.js │ ├── dataTables.bootstrap4.min.js │ ├── dataTables.buttons.min.js │ ├── dataTables.colReorder.min.js │ ├── jquery.dataTables.min.js │ ├── pdfmake.min.js │ └── vfs_fonts.js ├── apexcharts.min.js ├── blast_canvas_graph.js ├── bootstrap.min.js ├── datatable.js ├── download2.js ├── jquery.min.js ├── jszip.min.js ├── kinetic-v5.1.0.min.js ├── openGPlink.js └── popper.min.js ├── more.php ├── other_gene_ids.php ├── person_view.php ├── scripts ├── ImportModule.pm ├── create_annot_schema2.sql ├── import_annots_sch2.pl └── import_genes.pl ├── species.php ├── species_view.php ├── templates ├── annotations │ └── example │ │ └── gene_annotations.txt ├── apache │ └── easy_gdb_apache.conf ├── blast_dbs │ ├── category_1 │ │ ├── sample_blast_DB_genome.fasta │ │ ├── sample_blast_DB_genome.fasta.nhr │ │ ├── sample_blast_DB_genome.fasta.nin │ │ ├── sample_blast_DB_genome.fasta.nog │ │ ├── sample_blast_DB_genome.fasta.nsd │ │ ├── sample_blast_DB_genome.fasta.nsi │ │ └── sample_blast_DB_genome.fasta.nsq │ └── category_2 │ │ ├── sample_blast_DB_nucleotides.fasta │ │ ├── sample_blast_DB_nucleotides.fasta.nhr │ │ ├── sample_blast_DB_nucleotides.fasta.nin │ │ ├── sample_blast_DB_nucleotides.fasta.nog │ │ ├── sample_blast_DB_nucleotides.fasta.nsd │ │ ├── sample_blast_DB_nucleotides.fasta.nsi │ │ ├── sample_blast_DB_nucleotides.fasta.nsq │ │ ├── sample_blast_DB_proteins.fasta │ │ ├── sample_blast_DB_proteins.fasta.phr │ │ ├── sample_blast_DB_proteins.fasta.pin │ │ ├── sample_blast_DB_proteins.fasta.pog │ │ ├── sample_blast_DB_proteins.fasta.psd │ │ ├── sample_blast_DB_proteins.fasta.psi │ │ └── sample_blast_DB_proteins.fasta.psq ├── configuration_path.php ├── db_example_annotations │ ├── annotation_example_SwissProt.txt │ ├── annotation_example_TAIR10.txt │ └── gene_list.txt ├── downloads │ ├── Homo sapiens │ │ ├── Annotations │ │ │ └── gene_annotations.txt.gz │ │ └── Sequences │ │ │ ├── Homo_sapiens_v1.0_CDS.fasta.gz │ │ │ ├── Homo_sapiens_v1.0_PEP.fasta.gz │ │ │ ├── Homo_sapiens_v1.0_cDNA.fasta.gz │ │ │ └── Homo_sapiens_v1.0_genome.fasta.gz │ └── Species species 1 │ │ ├── Annotations │ │ └── gene_annotations.txt │ │ └── Sequences │ │ ├── Species_v1.0_CDS.fasta │ │ ├── Species_v1.0_PEP.fasta │ │ ├── Species_v1.0_cDNA.fasta │ │ ├── Species_v1.0_genome.fasta │ │ └── level 2 │ │ ├── level 3 │ │ ├── aa test_file_l3.fasta │ │ ├── level 4 │ │ │ ├── test_file_l4 copy.fasta │ │ │ └── test_file_l4.fasta │ │ ├── test_file_l3.fasta │ │ └── zz test_file_l3.fasta │ │ ├── test_file_l2 copy.fasta │ │ └── test_file_l2.fasta ├── egdb_files │ ├── css │ │ └── custom.css │ ├── egdb_conf │ │ ├── database_access.php │ │ └── easyGDB_conf.php │ ├── egdb_custom_text │ │ ├── about.php │ │ ├── custom_cookies.php │ │ ├── custom_footer.php │ │ ├── custom_pages │ │ │ ├── genome.php │ │ │ ├── other page.php │ │ │ ├── row_data.php │ │ │ ├── table_menu.php │ │ │ ├── table_to_page.php │ │ │ └── tables │ │ │ │ ├── table_example.txt │ │ │ │ └── table_example_2.txt │ │ ├── custom_toolbar.php │ │ ├── db_citation.php │ │ ├── expr_datasets │ │ │ ├── example1_description.php │ │ │ └── example2_description.php │ │ └── welcome_text.php │ ├── egdb_images │ │ ├── descriptors_imgs │ │ │ ├── Species_2 │ │ │ │ ├── sagarpa_flower_nectary_sessile.png │ │ │ │ ├── sagarpa_flower_nectary_stalked.png │ │ │ │ ├── sagarpa_flower_pollen_absent.png │ │ │ │ ├── sagarpa_flower_pollen_present.png │ │ │ │ ├── sagarpa_flower_style_kinked.png │ │ │ │ ├── sagarpa_flower_style_straight.png │ │ │ │ ├── sagarpa_inflorescence_color_lenticels_green.png │ │ │ │ ├── sagarpa_inflorescence_color_lenticels_red.png │ │ │ │ ├── sagarpa_inflorescence_flowering_type_help.png │ │ │ │ ├── sagarpa_inflorescence_length_axis_long.png │ │ │ │ ├── sagarpa_inflorescence_length_axis_medium.png │ │ │ │ ├── sagarpa_inflorescence_length_axis_short.png │ │ │ │ ├── sagarpa_leaf_blade_length_long.png │ │ │ │ ├── sagarpa_leaf_blade_length_medium.png │ │ │ │ ├── sagarpa_leaf_blade_length_short.png │ │ │ │ ├── sagarpa_leaf_blade_length_very_long.png │ │ │ │ ├── sagarpa_leaf_blade_length_very_short.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_large.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_length_width_large.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_length_width_medium.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_length_width_small.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_length_width_very_large.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_length_width_very_small.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_medium.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_small.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_very_large.png │ │ │ │ ├── sagarpa_leaf_blade_ratio_very_small.png │ │ │ │ ├── sagarpa_leaf_blade_shape_circular.png │ │ │ │ ├── sagarpa_leaf_blade_shape_elliptic.png │ │ │ │ ├── sagarpa_leaf_blade_shape_lanceolate.png │ │ │ │ ├── sagarpa_leaf_blade_shape_obovate.png │ │ │ │ ├── sagarpa_leaf_blade_shape_ovate.png │ │ │ │ ├── sagarpa_leaf_blade_width_broad.png │ │ │ │ ├── sagarpa_leaf_blade_width_medium.png │ │ │ │ ├── sagarpa_leaf_blade_width_narrow.png │ │ │ │ ├── sagarpa_leaf_blade_width_very_broad.png │ │ │ │ ├── sagarpa_leaf_blade_width_very_narrow.png │ │ │ │ ├── sagarpa_mature_fruit_diameter_large.png │ │ │ │ ├── sagarpa_mature_fruit_diameter_medium.png │ │ │ │ ├── sagarpa_mature_fruit_diameter_small.png │ │ │ │ ├── sagarpa_mature_fruit_diameter_very_large.png │ │ │ │ ├── sagarpa_mature_fruit_diameter_very_small.png │ │ │ │ ├── sagarpa_mature_fruit_glossiness_absent.png │ │ │ │ ├── sagarpa_mature_fruit_glossiness_medium.png │ │ │ │ ├── sagarpa_mature_fruit_glossiness_strong.png │ │ │ │ ├── sagarpa_mature_fruit_glossiness_weak.png │ │ │ │ ├── sagarpa_mature_fruit_length_long.png │ │ │ │ ├── sagarpa_mature_fruit_length_medium.png │ │ │ │ ├── sagarpa_mature_fruit_length_short.png │ │ │ │ ├── sagarpa_mature_fruit_length_very_long.png │ │ │ │ ├── sagarpa_mature_fruit_length_very_short.png │ │ │ │ ├── sagarpa_mature_fruit_presence_depression_stalk_end_absent.png │ │ │ │ ├── sagarpa_mature_fruit_presence_depression_stalk_end_present.png │ │ │ │ ├── sagarpa_mature_fruit_presence_neck_absent.png │ │ │ │ ├── sagarpa_mature_fruit_presence_neck_present.png │ │ │ │ ├── sagarpa_mature_fruit_ratio_large.png │ │ │ │ ├── sagarpa_mature_fruit_ratio_medium.png │ │ │ │ ├── sagarpa_mature_fruit_ratio_small.png │ │ │ │ ├── sagarpa_mature_fruit_ratio_very_large.png │ │ │ │ ├── sagarpa_mature_fruit_ratio_very_small.png │ │ │ │ ├── sagarpa_mature_fruit_shape_stalk_end_broadly_rounded.png │ │ │ │ ├── sagarpa_mature_fruit_shape_stalk_end_narrowly_rounded.png │ │ │ │ ├── sagarpa_mature_fruit_shape_stalk_end_pointed.png │ │ │ │ ├── sagarpa_mature_fruit_shape_stalk_end_truncate.png │ │ │ │ ├── sagarpa_mature_fruit_size_lenticels_medium.png │ │ │ │ ├── sagarpa_mature_fruit_surface_medium.png │ │ │ │ ├── sagarpa_mature_fruit_surface_rough.png │ │ │ │ ├── sagarpa_mature_fruit_surface_smooth.png │ │ │ │ ├── sagarpa_mature_fruit_surface_very_rough.png │ │ │ │ ├── sagarpa_mature_fruit_surface_very_smooth.png │ │ │ │ ├── sagarpa_ripe_fruit_adherence_skin_flesh_intermediate.png │ │ │ │ ├── sagarpa_ripe_fruit_adherence_skin_flesh_strong.png │ │ │ │ ├── sagarpa_ripe_fruit_adherence_skin_flesh_weak.png │ │ │ │ ├── sagarpa_ripe_fruit_anise_aroma_flesh_absent.png │ │ │ │ ├── sagarpa_ripe_fruit_anise_aroma_flesh_present.png │ │ │ │ ├── sagarpa_ripe_fruit_color_black.png │ │ │ │ ├── sagarpa_ripe_fruit_color_dark_green.png │ │ │ │ ├── sagarpa_ripe_fruit_color_dark_purple.png │ │ │ │ ├── sagarpa_ripe_fruit_color_dark_purple_or_black.png │ │ │ │ ├── sagarpa_ripe_fruit_color_layer_next_skin_light_green.png │ │ │ │ ├── sagarpa_ripe_fruit_color_layer_next_skin_medium_green.png │ │ │ │ ├── sagarpa_ripe_fruit_color_layer_next_skin_yellow_green.png │ │ │ │ ├── sagarpa_ripe_fruit_color_light_green.png │ │ │ │ ├── sagarpa_ripe_fruit_color_ligth_green.png │ │ │ │ ├── sagarpa_ripe_fruit_color_medium_green.png │ │ │ │ ├── sagarpa_ripe_fruit_color_medium_purple.png │ │ │ │ ├── sagarpa_ripe_fruit_color_reddish.png │ │ │ │ ├── sagarpa_ripe_fruit_color_yellow_green.png │ │ │ │ ├── sagarpa_ripe_fruit_consistency_skin_corky.png │ │ │ │ ├── sagarpa_ripe_fruit_consistency_skin_leathery.png │ │ │ │ ├── sagarpa_ripe_fruit_consistency_skin_membranous.png │ │ │ │ ├── sagarpa_ripe_fruit_main_color_flesh_cream.png │ │ │ │ ├── sagarpa_ripe_fruit_main_color_flesh_light_green.png │ │ │ │ ├── sagarpa_ripe_fruit_main_color_flesh_whitish.png │ │ │ │ ├── sagarpa_ripe_fruit_main_color_flesh_yellow.png │ │ │ │ ├── sagarpa_ripe_fruit_thickness_skin_medium.png │ │ │ │ ├── sagarpa_ripe_fruit_thickness_skin_moderately_thick.png │ │ │ │ ├── sagarpa_ripe_fruit_thickness_skin_moderately_thin.png │ │ │ │ ├── sagarpa_ripe_fruit_thickness_skin_very_thick.png │ │ │ │ └── sagarpa_ripe_fruit_thickness_skin_very_thin.png │ │ │ └── Species_3 │ │ │ │ ├── upov_inflorescence_number_primary_branches_help.png │ │ │ │ ├── upov_leaf_blade_shape_apex_acuminate.png │ │ │ │ ├── upov_leaf_blade_shape_apex_acute.png │ │ │ │ ├── upov_leaf_blade_shape_apex_attenuate.png │ │ │ │ ├── upov_leaf_blade_shape_base_acute.png │ │ │ │ ├── upov_leaf_blade_shape_base_obtuse.png │ │ │ │ ├── upov_leaf_blade_shape_base_rounded.png │ │ │ │ ├── upov_leaf_blade_shape_elliptic.png │ │ │ │ ├── upov_leaf_blade_shape_oblong.png │ │ │ │ ├── upov_leaf_blade_shape_ovate.png │ │ │ │ ├── upov_leaf_blade_twisting_absent.png │ │ │ │ ├── upov_leaf_blade_twisting_present.png │ │ │ │ ├── upov_mature_fruit_bulging_proximal_stylar_scar_help.png │ │ │ │ ├── upov_mature_fruit_bulging_ventral_shoulder_absent.png │ │ │ │ ├── upov_mature_fruit_bulging_ventral_shoulder_present.png │ │ │ │ ├── upov_mature_fruit_depth_groove_ventral_shoulder_help.png │ │ │ │ ├── upov_mature_fruit_point_stylar_scar_absent.png │ │ │ │ ├── upov_mature_fruit_point_stylar_scar_large.png │ │ │ │ ├── upov_mature_fruit_point_stylar_scar_medium.png │ │ │ │ ├── upov_mature_fruit_point_stylar_scar_small.png │ │ │ │ ├── upov_mature_fruit_presence_neck_absent.png │ │ │ │ ├── upov_mature_fruit_presence_neck_present.png │ │ │ │ ├── upov_mature_fruit_presence_sinus_absent.png │ │ │ │ ├── upov_mature_fruit_presence_sinus_present.png │ │ │ │ ├── upov_mature_fruit_ratio_help.png │ │ │ │ ├── upov_mature_fruit_shape_cross_section_broad_elliptic.png │ │ │ │ ├── upov_mature_fruit_shape_cross_section_circular.png │ │ │ │ ├── upov_mature_fruit_shape_cross_section_medium_elliptic.png │ │ │ │ ├── upov_mature_fruit_shape_dorsal_shoulder_falling_abruptly.png │ │ │ │ ├── upov_mature_fruit_shape_dorsal_shoulder_rounded_downward.png │ │ │ │ ├── upov_mature_fruit_shape_dorsal_shoulder_rounded_outward.png │ │ │ │ ├── upov_mature_fruit_shape_dorsal_shoulder_rounded_upward.png │ │ │ │ ├── upov_mature_fruit_shape_dorsal_shoulder_sloping_downward.png │ │ │ │ ├── upov_mature_fruit_stalk_cavity_absent.png │ │ │ │ ├── upov_mature_fruit_stalk_cavity_deep.png │ │ │ │ ├── upov_mature_fruit_stalk_cavity_medium.png │ │ │ │ ├── upov_mature_fruit_stalk_cavity_shallow.png │ │ │ │ ├── upov_seed_shape_lateral_view_oblong.png │ │ │ │ └── upov_seed_shape_lateral_view_reniform.png │ │ ├── easy_gdb_home.png │ │ ├── egdb_logo.png │ │ ├── expr │ │ │ ├── cartoons │ │ │ │ ├── tissue1.png │ │ │ │ ├── tissue2.png │ │ │ │ ├── tissue3.png │ │ │ │ └── tissue4.png │ │ │ ├── cold.jpeg │ │ │ ├── darkness.jpeg │ │ │ ├── drought.jpeg │ │ │ ├── fruit.jpeg │ │ │ ├── germinating_seed.jpeg │ │ │ ├── heat.jpeg │ │ │ ├── leaf.jpeg │ │ │ ├── peel.jpeg │ │ │ ├── root.jpeg │ │ │ └── seed.jpeg │ │ ├── favicon.ico │ │ ├── gallery │ │ │ ├── Species_2 │ │ │ │ └── ACC1 │ │ │ │ │ ├── fruit.jpg │ │ │ │ │ ├── fruit_ripe.jpg │ │ │ │ │ ├── fruit_ripe_open.jpg │ │ │ │ │ └── frut_unripe.jpg │ │ │ └── Species_3 │ │ │ │ └── ACC1 │ │ │ │ ├── Palmer_fruit.jpg │ │ │ │ └── Palmer_leaf.jpg │ │ ├── header_img.png │ │ ├── logos │ │ │ ├── Researchgate_icon.png │ │ │ ├── googlescholar.ico │ │ │ ├── logo1.png │ │ │ ├── logo2.png │ │ │ ├── logo3.png │ │ │ ├── logo4.png │ │ │ ├── ncbi.ico │ │ │ ├── orcid.ico │ │ │ └── twitter_icon.png │ │ ├── map_labels │ │ │ ├── Species_1_default.png │ │ │ ├── Species_2_default.png │ │ │ ├── Species_3_default.png │ │ │ ├── Species_3_green.png │ │ │ ├── Species_3_green_and_yellow.png │ │ │ ├── Species_3_orange.png │ │ │ ├── Species_3_orange_and_purple.png │ │ │ ├── Species_3_orange_and_red.png │ │ │ ├── Species_3_purple.png │ │ │ ├── Species_3_red.png │ │ │ ├── Species_3_red_and_purple.png │ │ │ ├── Species_3_yellow.png │ │ │ ├── Species_3_yellow_and_orange.png │ │ │ ├── Species_3_yellow_and_red.png │ │ │ ├── Species_3_yellow_green.png │ │ │ └── Species_3_yellow_orange.png │ │ ├── people │ │ │ ├── placeholder1.png │ │ │ └── placeholder2.png │ │ └── species │ │ │ ├── cherimoya.png │ │ │ ├── mango.png │ │ │ ├── olive.png │ │ │ ├── sp1.png │ │ │ ├── sp2.png │ │ │ └── sp3.png │ ├── egdb_labs │ │ └── person.php │ ├── egdb_species │ │ ├── cherimoya.php │ │ ├── custom_species_title.php │ │ ├── mango.php │ │ └── olive.php │ └── json_files │ │ ├── customization │ │ ├── custom_help.json │ │ ├── labs.json │ │ ├── logos.json │ │ └── species_list.json │ │ └── tools │ │ ├── annotation_links.json │ │ ├── blast_links.json │ │ ├── cartoons_example1.json │ │ ├── comparator_link.json │ │ ├── comparator_lookup.json │ │ ├── enrichment.json │ │ ├── expression_info.json │ │ └── vcf.json ├── expression_data │ ├── Example1 - Plant_gene_expression_RPKM.txt │ ├── Example1_2 - Plant_gene_expression_sample.txt │ ├── Example2 - Organism dataset name.txt │ ├── Example3 - Dataset with cartoons.txt │ └── comparator_gene_list.txt ├── jbrowse_example_data │ ├── gene_models.gff │ ├── genome.fasta │ ├── jbrowse.conf │ ├── trackList.json │ └── tracks.conf ├── lookup │ ├── Species1_Arabidopsis_Best_hit.txt │ ├── Species_name1_v3_to_Species_name1_v1.txt │ └── Species_name1_v3_to_Species_name1_v2.txt ├── passport │ └── example │ │ ├── Species_1 │ │ ├── Flower_descriptors.txt │ │ ├── Fruit_descriptors.txt │ │ ├── Leaf_descriptors.txt │ │ ├── passport.json │ │ └── sp1_passport.txt │ │ ├── Species_2 │ │ ├── Inflorescence_descriptors.txt │ │ ├── Leaf_descriptors.txt │ │ ├── Mature_fruit_descriptors.txt │ │ ├── Ripe_fruit_descriptors.txt │ │ ├── convert_numeric_to_cathegoric.json │ │ ├── featured_descriptors.json │ │ ├── passport.json │ │ ├── sp2_passport.txt │ │ ├── sp2_phenotype_imgs.json │ │ └── translator.json │ │ ├── Species_3 │ │ ├── Phenotype_descriptors.txt │ │ ├── convert_numeric_to_cathegoric.json │ │ ├── passport.json │ │ ├── sp3_passport.txt │ │ ├── sp3_phenotype_imgs.json │ │ └── translator.json │ │ └── germplasm_list.json └── private_expression_data │ └── private_example1.txt ├── toolbar.php └── tools ├── annot_input_list.php ├── annot_output_db.php ├── annot_output_file.php ├── blast ├── blast_dbs_select.php ├── blast_input.php ├── blast_output.php ├── blast_output_multiple.php ├── blast_output_single.php ├── blastdbcmd.php ├── blastdbcmd_multiple.php ├── blastdbcmd_single.php ├── get_dbs.php └── loading_blast.php ├── coexpression ├── ajax_get_names_array.php ├── coex_input.php ├── coex_modal.php ├── coex_operations.php └── coex_output.php ├── common_functions.php ├── download_files.php ├── expression ├── 01_expr_check_dataset_description.php ├── 01_expr_colors_range.php ├── 01_expr_load_description.php ├── 02_expr_load_annotations.php ├── 02_expr_load_db_annotations.php ├── 03_expr_load_avg_table_html.php ├── 03_expr_load_cards_html.php ├── 03_expr_load_cartoons_html.php ├── 03_expr_load_heatmap_html.php ├── 03_expr_load_lines_html.php ├── 03_expr_load_replicates_html.php ├── ajax_cards.php ├── ajax_get_names_array.php ├── card_pattern.png ├── cartoons_kinetic.js ├── comparator_input.php ├── comparator_output.php ├── expr_placeholder.jpeg ├── expression_graphs.js ├── expression_input.php ├── expression_input_private.php ├── expression_menu.php ├── expression_output.php └── expression_output_private.php ├── fasta_download.php ├── gene_enrichment.php ├── gene_enrichment_ajax.php ├── gene_lookup.php ├── gene_lookup_output.php ├── get_annotation_types.php ├── modal.html ├── passport ├── 01_list_pass_files.php ├── 02_pass_file_to_datatable.php ├── 03_passport_and_phenotype.php ├── ajax_search_avanced.php ├── country_coordinates.txt ├── gallery.php ├── map.php ├── multi_map.php ├── passport_ajax.php ├── passport_search_input.php ├── passport_search_output.php ├── passport_search_output_avanced.php ├── passport_search_phenotypes.php ├── passport_table_ajax.php └── view_subdirectories.php ├── search ├── search_annot.php ├── search_info_modal.php ├── search_input.php ├── search_output.php └── search_output_file.php └── vcf ├── ajax_get_gene_coordinates.php ├── vcf_ajax_acc_data.php ├── vcf_extract_input.php ├── vcf_extract_output.php └── vcf_id_extract_output.php /.gitignore: -------------------------------------------------------------------------------- 1 | # OS generated files # 2 | ###################### 3 | .DS_Store 4 | .DS_Store? 5 | ._* 6 | .Spotlight-V100 7 | .Trashes 8 | ehthumbs.db 9 | Thumbs.db 10 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2021 Noé Fernández Pozo 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /about.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 7 |
8 |
9 | 10 |
11 |
12 | 13 | 0) { 15 | include_once realpath("$custom_text_path/db_citation.php"); 16 | } 17 | ?> 18 | 19 |
20 |
21 | 22 | 27 |
28 |
29 | 30 |
31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /cookies.php: -------------------------------------------------------------------------------- 1 | 2 | 3 |
4 | 5 |
6 |

Cookies

7 |
8 | 9 | "; 15 | echo "This site only uses functional cookies required for login control and needed cookies from third party tools such as JBrowse. 16 | JBrowse uses cookies to remember your configuration in the genome browser, such as the tracks loaded and the position in the genome. 17 | When using this site you accept the use of the cookies."; 18 | echo "

"; 19 | } 20 | ?> 21 |
22 | 23 | 24 | -------------------------------------------------------------------------------- /css/datatables/colReorder.dataTables.min.css: -------------------------------------------------------------------------------- 1 | table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:rgba(255, 255, 255, 0.7);z-index:202}div.DTCR_pointer{width:1px;background-color:#0259c4;z-index:201} 2 | -------------------------------------------------------------------------------- /css/loading_datatable.css: -------------------------------------------------------------------------------- 1 | /* HTML:
*/ 2 | .loader { 3 | font-weight: bold; 4 | font-family: sans-serif; 5 | font-size: 20px; 6 | animation: l1 1s linear infinite alternate; 7 | text-align: center; 8 | } 9 | .loader:before { 10 | content:"Loading..."; 11 | } 12 | @keyframes l1 {to{opacity: 0}} -------------------------------------------------------------------------------- /custom_view.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
5 | 6 | 7 |
8 |
9 | 14 |
15 |
16 | 17 |
18 | 19 | -------------------------------------------------------------------------------- /downloads.php: -------------------------------------------------------------------------------- 1 | 2 |

3 |
4 |

Download Files

5 |
6 |
7 | 8 |
9 |
10 |
11 | 12 | -------------------------------------------------------------------------------- /favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/favicon.ico -------------------------------------------------------------------------------- /footer.php: -------------------------------------------------------------------------------- 1 | 2 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /gene_seq.php: -------------------------------------------------------------------------------- 1 |
2 | Sequences 3 |
4 | 5 |
6 | 7 | 8 | $blast_dir"; 20 | 21 | $dbs_found = get_dir_and_files($bdb_path.'/'.$blast_dir); 22 | asort($dbs_found); 23 | 24 | foreach ($dbs_found as $bdb) { 25 | //echo "
$bdb
"; 26 | 27 | if ( preg_match('/\.nhr$|\.phr$/', $bdb, $match) ) { 28 | $bdb = str_replace(".phr","",$bdb); 29 | $bdb = str_replace(".nhr","",$bdb); 30 | $full_path_db = $bdb_path.'/'.$blast_dir."/".$bdb; 31 | 32 | exec("blastdbcmd -db {$full_path_db} -entry " . escapeshellarg($gene_name) ."| sed 's/lcl|//'" ,$ret); 33 | 34 | if ($ret) { 35 | $blast_db = str_replace(".fasta","",$bdb); 36 | $blast_db = str_replace("_"," ",$blast_db); 37 | 38 | if (preg_match('/^category_\d/', $blast_dir, $match) ) { 39 | echo "
$blast_db
"; 40 | } else { 41 | $blast_category = str_replace("_"," ",$blast_dir); 42 | echo "
$blast_category, $blast_db
"; 43 | } 44 | echo "
"; 45 | echo "
".implode("
",$ret)."
"; 46 | echo "

"; 47 | } 48 | $ret=null; 49 | } 50 | 51 | } // close foreach 52 | } 53 | } 54 | 55 | 56 | ?> 57 |
58 |
59 | -------------------------------------------------------------------------------- /help/03_genome_browser.php: -------------------------------------------------------------------------------- 1 | 3 | 4 |
5 |
6 |
7 | Go to help 8 |
9 |
10 |

Genome Browser

11 |
12 | 13 |

14 | JBrowse is an external app to IHSM Subtropical DB. Because of that, it appears an emergent window with the advice of cookies policy (Figure 1). 15 | Clicking in OK it will redirect to the JBrowse page, it will open in a new tab. 16 | Once inside, the user can browse in the genoma chosen with the different tracks available, zoom in the genome or search a specific gene (with de dropdown or autocomplete search bar) (Figure 2). 17 | More information can be consulted in 18 |

19 |
  • 20 | User guide of JBrowse 21 |
    • 22 | 23 |
    24 | 25 |
    26 | Figure 1. Cookies policy to accept. 27 |
    28 |
    29 |
    30 |
    31 |
    32 | 33 |
    34 | Figure 2. JBrowse example. 35 |
    36 |
    37 |
    38 |
    39 | 42 |
    43 | 44 | 45 | -------------------------------------------------------------------------------- /help/04_sequence_extraction.php: -------------------------------------------------------------------------------- 1 | 3 | 4 |
    5 |
    6 |
    7 | Go to help 8 |
    9 |
    10 |

    Sequence Extraction

    11 |
    12 |

    13 | This tool enables the user to download a list of gene identifiers (IDs). 14 | It is works pasting the gene ID and picking the appropriate Dataset (Figure 1). Multiple gene ID can be pasted into the box. 15 | Once done, clicking on Download button, the file will download in FASTA format. 16 |

    17 |
    18 | 19 |
    20 | Figure 1. Sequence_extraction main page. 21 |
    22 |
    23 |
    24 |
    25 | 28 |
    29 | 30 | 31 | -------------------------------------------------------------------------------- /help/05_annotation_extraction.php: -------------------------------------------------------------------------------- 1 | 3 | 4 |
    5 |
    6 |
    7 | Go to help 8 |
    9 |
    10 |

    Annotation Extraction

    11 |
    12 |

    13 | The main page of the annotation extraction (Figure 1) allows the user to search a list of genes identifiers (IDs) and obtain the annotations from different databases (SwissProt, Araport11, TrEMBL and InterPro). 14 | Multiple gene ID can be pasted into the box. Clicking on Search button, it will get the outputs. 15 | Then, the user can access to an input clicking on the database ID (Figure 2), it will redirect to the database page (in a new tab) to get more information. 16 | The output results can be copied to the clipboard, downloaded in several formats (CVS, Excel or PDF) and printed. The user can configurate, in the Column visibility dropdown, which database appears. 17 |

    18 |
    19 | 20 |
    21 | Figure 1. Annotation extraction main page. 22 |
    23 |
    24 |
    25 | 26 |
    27 | Figure 2. Annotation extraction output example. 28 |
    29 |
    30 |
    31 |
    32 | 35 |
    36 | 37 | 38 | -------------------------------------------------------------------------------- /help/06_gene_lookup.php: -------------------------------------------------------------------------------- 1 | 3 | 4 |
    5 |
    6 |
    7 | Go to help 8 |
    9 |
    10 |

    Gene Version Lookup

    11 |
    12 |

    13 | The gene version lookup tool enable the user to compare between gene version from same gene or different species genes, it searches the equivalence gene. 14 | It searches the most similar gene based on proteins because of the genetic code conservation. 15 |

    16 |
    17 |

    18 | The gene version lookup tool (Figure 1) allows the user to provide a list of genes and select one of the available datasets to get those gene IDs in the version of the required genome. 19 | Clicking on the search button will return the table output for those genes. 20 | This table can be downloaded in several formats (CSV, Excel, PDF), can be copied to the clipboard, filtering out unwanted columns and searching within the information in the table. 21 |

    22 |
    23 | 24 |
    25 | Figure 1. Gene version lookup main page. 26 |
    27 |
    28 |
    29 |
    30 | 33 |
    34 | 35 | 36 | -------------------------------------------------------------------------------- /help/07_gene_enrichment.php: -------------------------------------------------------------------------------- 1 | 3 | 4 |
    5 |
    6 |
    7 | Go to help 8 |
    9 |
    10 |

    Gene Set Enrichment

    11 |
    12 |

    13 | The gene set enrichment is a tool similar to gene lookup, it is possible to turn some genes to others. 14 | The main page of the gene set enrichment (Figure 1) allows the user to provide a list of genes to perform statistical enrichment analysis in g:Profiler. 15 | Multiple gene names can be pasted into the box. Then, the user can choose one of the species available for Gene Ontology enrichment and convert their gene IDs in case they are not of any of the species supplied. 16 | Clicking on the Submit button will redirect the user to the g:Profiler main page, in a new tab, where the analysis will be made (Figure 2). 17 | For more info, consult: Welcome to g:Profiler 18 |

    19 |
    20 | 21 |
    22 | Figure 1. Gene set enrichment main page. 23 |
    24 |
    25 |
    26 | 27 |
    28 | Figure 2. Gene set enrichment output example. 29 |
    30 |
    31 |
    32 |
    33 |
    34 | 37 |
    38 | 39 | 40 | -------------------------------------------------------------------------------- /help/10_coexpression.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
    5 | 6 | 7 | Go to help 8 | 9 |
    10 | 11 |
    12 |

    13 |

    Coexpression Search

    14 |

    15 | The coexpression search tool allows users to explore genes with similar expression profiles across selected datasets (Figure 1). By simply entering a gene ID, users can retrieve a table of correlated genes based on predefined thresholds (e.g. Pearson correlation > 0.8). 16 | The tool is particularly useful to investigate potential functional relationships or regulatory modules within a species. 17 |

    18 | 19 |
    20 | 21 |
    22 | Figure 1. Coexpression search main page. 23 |


    24 |
    25 | 26 |

    27 | Results are displayed in an interactive table (Figure 2) that supports sorting, filtering, and exporting. Users can download the table in multiple formats (CSV, Excel, PDF), or copy/print the results directly. 28 | Clicking on a gene ID in the results will redirect to its detailed gene page. 29 |

    30 | 31 |
    32 | 33 |
    34 | Figure 2. Example of coexpression results table with interactive features. 35 |


    36 |
    37 |
    38 | 39 | 40 | -------------------------------------------------------------------------------- /help/header_help.php: -------------------------------------------------------------------------------- 1 | 9 | 10 | <?php echo "$dbTitle";?> 11 | 12 | 13 | > 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | "; 24 | } 25 | ?> 26 | -------------------------------------------------------------------------------- /help/help_images/JBrowse_cookies.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/help/help_images/JBrowse_cookies.png -------------------------------------------------------------------------------- /help/help_images/JBrowse_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/help/help_images/JBrowse_example.png 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https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/help/help_images/sequence_extraction.png -------------------------------------------------------------------------------- /index.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /install/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM php:7.4-apache 2 | 3 | RUN apt-get update -y 4 | RUN apt-get install libpq-dev -y 5 | RUN apt-get install git -y 6 | RUN apt-get install zlib1g-dev -y 7 | RUN apt-get install libexpat1-dev -y 8 | 9 | 10 | RUN docker-php-ext-configure pgsql -with-pgsql=/usr/local/pgsql 11 | RUN docker-php-ext-install pdo pdo_pgsql pgsql 12 | 13 | RUN apt-get install ncbi-blast+ -y 14 | RUN apt-get install vim -y 15 | RUN apt-get install less -y 16 | RUN apt-get install wget -y 17 | RUN apt-get install zip -y 18 | 19 | RUN apt-get install cpanminus -y 20 | RUN cpanm DBI 21 | RUN cpanm Term::ReadKey 22 | RUN cpanm DBD::Pg 23 | 24 | # Needed for JBrowse 25 | RUN cpanm local::lib 26 | RUN cpanm PerlIO::gzip 27 | RUN apt-get install libhash-merge-perl libjson-xs-perl libjson-perl liblist-moreutils-perl libperlio-gzip-perl libparse-recdescent-perl liblocal-lib-perl libxml-parser-perl libbio-perl-perl -y 28 | CMD ["apache2-foreground"] -------------------------------------------------------------------------------- /install/docker-compose.yml: -------------------------------------------------------------------------------- 1 | version: "3.9" 2 | 3 | services: 4 | easy_gdb: 5 | build: 6 | context: . 7 | container_name: easy_gdb 8 | ports: 9 | - "8000:80" 10 | volumes: 11 | - ./src:/var/www/html 12 | DB: 13 | image: postgres 14 | container_name: DB 15 | ports: 16 | - "5432:5432" 17 | restart: always 18 | environment: 19 | - POSTGRES_PASSWORD=1234 20 | -------------------------------------------------------------------------------- /install/easy_gdb_apache.conf: -------------------------------------------------------------------------------- 1 | 2 | # The ServerName directive sets the request scheme, hostname and port that 3 | # the server uses to identify itself. This is used when creating 4 | # redirection URLs. In the context of virtual hosts, the ServerName 5 | # specifies what hostname must appear in the request's Host: header to 6 | # match this virtual host. For the default virtual host (this file) this 7 | # value is not decisive as it is used as a last resort host regardless. 8 | # However, you must set it for any further virtual host explicitly. 9 | #ServerName www.example.com 10 | 11 | ServerAdmin webmaster@localhost 12 | DocumentRoot /var/www/html 13 | 14 | # Available loglevels: trace8, ..., trace1, debug, info, notice, warn, 15 | # error, crit, alert, emerg. 16 | # It is also possible to configure the loglevel for particular 17 | # modules, e.g. 18 | #LogLevel info ssl:warn 19 | 20 | ErrorLog ${APACHE_LOG_DIR}/error.log 21 | CustomLog ${APACHE_LOG_DIR}/access.log combined 22 | 23 | # For most configuration files from conf-available/, which are 24 | # enabled or disabled at a global level, it is possible to 25 | # include a line for only one particular virtual host. For example the 26 | # following line enables the CGI configuration for this host only 27 | # after it has been globally disabled with "a2disconf". 28 | #Include conf-available/serve-cgi-bin.conf 29 | 30 | 31 | AuthType Basic 32 | AuthName "Restricted Content" 33 | AuthUserFile /etc/apache2/.htpasswd 34 | Require valid-user 35 | 36 | 37 | 38 | -------------------------------------------------------------------------------- /jb_frame.php: -------------------------------------------------------------------------------- 1 | Genome Browser'; 10 | echo '
    '; 11 | 12 | $jb_gene_name = $gene_name; 13 | 14 | echo "Full screen"; 15 | echo ""; 17 | echo '
    '; 18 | } 19 | ?> 20 | 21 | 22 | 30 | -------------------------------------------------------------------------------- /jb_frame_file.php: -------------------------------------------------------------------------------- 1 | 1) { 29 | // echo "

    Several JBrowse datasets were found

    "; 30 | // } 31 | 32 | if ($counter == 1) { 33 | echo '
    Genome Browser
    '; 34 | echo '
    '; 35 | 36 | echo "Full screen"; 37 | echo ""; 39 | echo '
    '; 40 | } 41 | 42 | } 43 | ?> 44 | 45 | 53 | -------------------------------------------------------------------------------- /js/Datatables/buttons.bootstrap4.min.js: -------------------------------------------------------------------------------- 1 | /*! 2 | Bootstrap integration for DataTables' Buttons 3 | ©2016 SpryMedia Ltd - datatables.net/license 4 | */ 5 | (function(c){"function"===typeof define&&define.amd?define(["jquery","datatables.net-bs4","datatables.net-buttons"],function(a){return c(a,window,document)}):"object"===typeof exports?module.exports=function(a,b){a||(a=window);b&&b.fn.dataTable||(b=require("datatables.net-bs4")(a,b).$);b.fn.dataTable.Buttons||require("datatables.net-buttons")(a,b);return c(b,a,a.document)}:c(jQuery,window,document)})(function(c,a,b,f){a=c.fn.dataTable;c.extend(!0,a.Buttons.defaults,{dom:{container:{className:"dt-buttons btn-group flex-wrap"}, 6 | button:{className:"btn btn-secondary"},collection:{tag:"div",className:"dropdown-menu",button:{tag:"a",className:"dt-button dropdown-item",active:"active",disabled:"disabled"}}},buttonCreated:function(e,d){return e.buttons?c('
    ').append(d):d}});a.ext.buttons.collection.className+=" dropdown-toggle";a.ext.buttons.collection.rightAlignClassName="dropdown-menu-right";return a.Buttons}); 7 | -------------------------------------------------------------------------------- /js/Datatables/buttons.print.min.js: -------------------------------------------------------------------------------- 1 | /*! 2 | Print button for Buttons and DataTables. 3 | 2016 SpryMedia Ltd - datatables.net/license 4 | */ 5 | (function(b){"function"===typeof define&&define.amd?define(["jquery","datatables.net","datatables.net-buttons"],function(c){return b(c,window,document)}):"object"===typeof exports?module.exports=function(c,g){c||(c=window);g&&g.fn.dataTable||(g=require("datatables.net")(c,g).$);g.fn.dataTable.Buttons||require("datatables.net-buttons")(c,g);return b(g,c,c.document)}:b(jQuery,window,document)})(function(b,c,g,y){var u=b.fn.dataTable,n=g.createElement("a"),v=function(a){n.href=a;a=n.host;-1===a.indexOf("/")&& 6 | 0!==n.pathname.indexOf("/")&&(a+="/");return n.protocol+"//"+a+n.pathname+n.search};u.ext.buttons.print={className:"buttons-print",text:function(a){return a.i18n("buttons.print","Print")},action:function(a,k,p,h){a=k.buttons.exportData(b.extend({decodeEntities:!1},h.exportOptions));p=k.buttons.exportInfo(h);var w=k.columns(h.exportOptions.columns).flatten().map(function(d){return k.settings()[0].aoColumns[k.column(d).index()].sClass}).toArray(),r=function(d,e){for(var x="",l=0,z=d.length;l"+(null===d[l]||d[l]===y?"":d[l])+"";return x+""},m='';h.header&&(m+=""+r(a.header,"th")+"");m+="";for(var t=0,A=a.body.length;t";h.footer&&a.footer&&(m+=""+r(a.footer,"th")+"");m+="
    ";var f=c.open("","");f.document.close();var q=""+p.title+"";b("style, link").each(function(){var d=q,e=b(this).clone()[0]; 8 | "link"===e.nodeName.toLowerCase()&&(e.href=v(e.href));q=d+e.outerHTML});try{f.document.head.innerHTML=q}catch(d){b(f.document.head).html(q)}f.document.body.innerHTML="

    "+p.title+"

    "+(p.messageTop||"")+"
    "+m+"
    "+(p.messageBottom||"")+"
    ";b(f.document.body).addClass("dt-print-view");b("img",f.document.body).each(function(d,e){e.setAttribute("src",v(e.getAttribute("src")))});h.customize&&h.customize(f,h,k);a=function(){h.autoPrint&&(f.print(),f.close())};navigator.userAgent.match(/Trident\/\d.\d/)? 9 | a():f.setTimeout(a,1E3)},title:"*",messageTop:"*",messageBottom:"*",exportOptions:{},header:!0,footer:!1,autoPrint:!0,customize:null};return u.Buttons}); 10 | -------------------------------------------------------------------------------- /js/openGPlink.js: -------------------------------------------------------------------------------- 1 | var openGPlink = function(url, data) { 2 | // open g:Profiler with prepopulated values 3 | // 4 | // url - the tool we are targeting. Usually one of 5 | // 'https://biit.cs.ut.ee/gprofiler/gost' 6 | // 'https://biit.cs.ut.ee/gprofiler/convert' 7 | // 'https://biit.cs.ut.ee/gprofiler/orth' 8 | // 'https://biit.cs.ut.ee/gprofiler/snpense' 9 | // Could also direct to beta ('https://biit.cs.ut.ee/gprofiler_beta/gost') 10 | // or recent archives ('https://biit.cs.ut.ee/gprofiler_archive3/e100_eg47_p14/gost') 11 | // 12 | // data - javascript object with endpoint-appropriate fields filled 13 | // see https://biit.cs.ut.ee/gprofiler/page/apis 14 | // 15 | // Example: 16 | // 17 | // openGPlink('https://biit.cs.ut.ee/gprofiler/convert', 18 | // {query: ['FBgn0016984'], organism:'dmelanogaster', target:'GO', numeric_namespace:'ENTREZGENE'} 19 | // ) 20 | 21 | // add an invisible form to the DOM 22 | var form = document.createElement('form') 23 | // request gets made to the gplink service, no data is stored on the server 24 | form.setAttribute('action', 'https://biit.cs.ut.ee/gplink/p') 25 | form.setAttribute('method', 'post') 26 | form.setAttribute('name', 'gp_submit_form') 27 | form.setAttribute('id', 'gp_submit_form') 28 | form.setAttribute('target', '_blank') 29 | 30 | var payload = document.createElement('input') 31 | payload.setAttribute('type', 'text') 32 | payload.setAttribute('name', 'payload') 33 | payload.setAttribute('value', JSON.stringify(data)) 34 | payload.setAttribute('hidden', '') 35 | 36 | var urlElement = document.createElement('input') 37 | urlElement.setAttribute('type', 'text') 38 | urlElement.setAttribute('name', 'url') 39 | urlElement.setAttribute('value', url) 40 | urlElement.setAttribute('hidden', '') 41 | 42 | form.appendChild(payload) 43 | form.appendChild(urlElement) 44 | 45 | document.body.appendChild(form) 46 | 47 | // submit the form. This should open g:Profiler in a new tab with values prepopulated. 48 | form.submit() 49 | 50 | // remove the form from DOM 51 | form.parentNode.removeChild(form) 52 | } 53 | -------------------------------------------------------------------------------- /more.php: -------------------------------------------------------------------------------- 1 |
  • 2 | More 3 |
    4 | 5 | '.$toolbar_name.''; 13 | } 14 | 15 | } 16 | 17 | } 18 | ?> 19 | 20 |
    21 |
    • 22 | 23 | -------------------------------------------------------------------------------- /other_gene_ids.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
    5 | Other Gene Versions 6 |
    7 | 8 |
    9 |
    10 | 11 |

    GENE ID: $gene_id



    \n\n"; 13 | 14 | $gene_id_query = "SELECT * FROM gene join gene_version ON (gene.gene_version_id=gene_version.gene_version_id) JOIN gene_gene ON(gene_id=gene_id2) WHERE gene_id1='".pg_escape_string($gene_id)."' ORDER BY gene_version ASC"; 15 | // $gene_id_query = "SELECT * FROM gene JOIN gene_gene ON(gene_id=gene_id2) WHERE gene_id1='$gene_id' ORDER BY genome_version DESC, gene_name ASC"; 16 | $gid_res = pg_query($gene_id_query) or die('Query failed: ' . pg_last_error()); 17 | 18 | if ($gid_res) { 19 | // Printing results in HTML 20 | echo "\n\n"; 21 | 22 | while ($line = pg_fetch_array($gid_res, null, PGSQL_ASSOC)) { 23 | $old_gene_name = $line["gene_name"]; 24 | $gene_version = $line["gene_version"]; 25 | $version_class = str_replace(".","_",$gene_version); 26 | echo "\n"; 27 | // echo "\n"; 28 | } 29 | 30 | echo "
    Gene NameVersion
    $old_gene_name$gene_version
    $old_gene_name$gene_version
    \n\n"; 31 | 32 | // Free resultset 33 | pg_free_result($gid_res); 34 | } 35 | 36 | ?> 37 | 38 |
    39 |
    40 | 41 | 55 | -------------------------------------------------------------------------------- /person_view.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
    5 |
    6 | 7 | 8 |
    9 |
    10 | 11 |
    12 |
    13 | 14 | 15 |
    16 | 17 |
    18 | 19 | -------------------------------------------------------------------------------- /scripts/create_annot_schema2.sql: -------------------------------------------------------------------------------- 1 | CREATE TABLE species ( 2 | species_id bigserial PRIMARY KEY, 3 | species_name varchar(80) UNIQUE NOT NULL, 4 | jbrowse_folder varchar(80) UNIQUE 5 | ); 6 | 7 | CREATE TABLE annotation_version ( 8 | annotation_version_id bigserial PRIMARY KEY, 9 | annotation_version varchar(80) NOT NULL 10 | ); 11 | 12 | CREATE TABLE gene ( 13 | gene_id bigserial PRIMARY KEY, 14 | gene_name varchar(80) UNIQUE NOT NULL, 15 | annotation_version_id bigserial REFERENCES annotation_version(annotation_version_id), 16 | species_id bigserial REFERENCES species(species_id) 17 | ); 18 | 19 | CREATE TABLE annotation_type ( 20 | annotation_type_id bigserial PRIMARY KEY, 21 | annotation_type varchar(80) UNIQUE NOT NULL 22 | ); 23 | 24 | CREATE TABLE annotation ( 25 | annotation_id bigserial PRIMARY KEY, 26 | annotation_term varchar(80) UNIQUE, 27 | annotation_desc text NOT NULL, 28 | annotation_type_id bigserial REFERENCES annotation_type(annotation_type_id) 29 | ); 30 | 31 | CREATE TABLE gene_annotation ( 32 | gene_annotation_id bigserial PRIMARY KEY, 33 | gene_id bigserial REFERENCES gene(gene_id), 34 | annotation_id bigserial REFERENCES annotation(annotation_id) 35 | ); 36 | 37 | 38 | -- 39 | GRANT ALL PRIVILEGES ON species TO web_usr; 40 | GRANT ALL PRIVILEGES ON annotation_version TO web_usr; 41 | GRANT ALL PRIVILEGES ON annotation_type TO web_usr; 42 | GRANT ALL PRIVILEGES ON gene TO web_usr; 43 | GRANT ALL PRIVILEGES ON annotation TO web_usr; 44 | GRANT ALL PRIVILEGES ON gene_annotation TO web_usr; 45 | 46 | -- Index 47 | CREATE EXTENSION IF NOT EXISTS pg_trgm; 48 | CREATE INDEX annotation_idx ON annotation USING gin(annotation_desc gin_trgm_ops); 49 | CREATE INDEX idx_lower_gname ON gene (lower(gene_name)) 50 | -------------------------------------------------------------------------------- /scripts/import_genes.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | use strict; 4 | use warnings; 5 | 6 | use DBI; 7 | use Term::ReadKey; 8 | use File::Basename; 9 | use lib dirname (__FILE__); 10 | use ImportModule; 11 | 12 | # check arguments and print usage 13 | if (scalar(@ARGV) != 4) { 14 | print "Usage: perl import_genes.pl \n\n"; 15 | print "Example: perl import_genes.pl gene_list.txt \"Mola mola\" \"1.0\" \"easy_gdb_sample\" \n"; 16 | exit; 17 | } 18 | 19 | # save arguments in variables 20 | my ($gene_file,$species,$annotation_v,$jbrowse_folder) = @ARGV; 21 | 22 | # ImportModule::hello_world(); 23 | # ImportModule::print_sps($species); 24 | 25 | my $username="postgres"; 26 | 27 | print "host name (postgres container name)> "; 28 | my $host=; 29 | print "\n"; 30 | chomp($host); 31 | 32 | 33 | print "DB name> "; 34 | my $dbname=; 35 | print "\n"; 36 | chomp($dbname); 37 | 38 | print "Password> "; 39 | ReadMode 'noecho'; # Disable echoing 40 | my $password=; 41 | ReadMode 'original'; # Turn it back on 42 | 43 | print "\n"; 44 | chomp($password); 45 | 46 | my $dbh = DBI->connect("dbi:Pg:dbname=$dbname;host=$host;", "$username", "$password"); 47 | $dbh->begin_work; 48 | 49 | my $species_id = ImportModule::check_species($dbh,$species); 50 | if (!$species_id) { 51 | $species_id = ImportModule::insert_species($dbh,$species,$jbrowse_folder); 52 | } 53 | 54 | my $annot_v_id = ImportModule::check_annotation_version($dbh,$annotation_v); 55 | if (!$annot_v_id) { 56 | $annot_v_id = ImportModule::insert_annotation_version($dbh,$annotation_v); 57 | } 58 | 59 | open (my $fh2, $gene_file) || die ("\nERROR: the file $gene_file could not be found\n"); 60 | 61 | while (my $line = <$fh2>) { 62 | chomp($line); 63 | 64 | $line =~ s/^\s*//; 65 | $line =~ s/\s*$//; 66 | 67 | my $gene_name = $line; 68 | my $gene_id = ImportModule::check_gene($dbh,$gene_name,$species_id,$annot_v_id); 69 | 70 | if (!$gene_id) { 71 | ImportModule::insert_gene($dbh,$gene_name,$species_id,$annot_v_id); 72 | } 73 | 74 | } #end of file 75 | 76 | $dbh->commit; 77 | $dbh->disconnect; 78 | -------------------------------------------------------------------------------- /species.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | '; 8 | echo '

    Species

    '; 9 | } 10 | ?> 11 | 12 |
    13 | 14 | $value) { 21 | 22 | if ($species_hash[$key]["public"]) { 23 | echo ''; 24 | // echo ''; 25 | echo ''.$species_hash[$key]['; 26 | echo '
    '; 27 | echo '
    '.$species_hash[$key]["card_title"].'
    '; 28 | echo '
    '.$species_hash[$key]["card_subtitle"].'
    '; 29 | echo '
    '; 30 | echo '    '; 31 | } 32 | 33 | } 34 | 35 | } 36 | ?> 37 | 38 |
    39 |
    40 | 41 | -------------------------------------------------------------------------------- /species_view.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 18 | 19 |
    20 | 21 |
    22 | 23 | -------------------------------------------------------------------------------- /templates/apache/easy_gdb_apache.conf: -------------------------------------------------------------------------------- 1 | 2 | # The ServerName directive sets the request scheme, hostname and port that 3 | # the server uses to identify itself. This is used when creating 4 | # redirection URLs. In the context of virtual hosts, the ServerName 5 | # specifies what hostname must appear in the request's Host: header to 6 | # match this virtual host. For the default virtual host (this file) this 7 | # value is not decisive as it is used as a last resort host regardless. 8 | # However, you must set it for any further virtual host explicitly. 9 | #ServerName www.example.com 10 | 11 | ServerAdmin webmaster@localhost 12 | DocumentRoot /var/www/html 13 | 14 | # Available loglevels: trace8, ..., trace1, debug, info, notice, warn, 15 | # error, crit, alert, emerg. 16 | # It is also possible to configure the loglevel for particular 17 | # modules, e.g. 18 | #LogLevel info ssl:warn 19 | 20 | ErrorLog ${APACHE_LOG_DIR}/error.log 21 | CustomLog ${APACHE_LOG_DIR}/access.log combined 22 | 23 | # For most configuration files from conf-available/, which are 24 | # enabled or disabled at a global level, it is possible to 25 | # include a line for only one particular virtual host. For example the 26 | # following line enables the CGI configuration for this host only 27 | # after it has been globally disabled with "a2disconf". 28 | #Include conf-available/serve-cgi-bin.conf 29 | 30 | # 31 | # AuthType Basic 32 | # AuthName "Restricted Content" 33 | # AuthUserFile /etc/apache2/.htpasswd 34 | # Require valid-user 35 | # 36 | 37 | 38 | AuthType Basic 39 | AuthName "Private Web Site" 40 | AuthUserFile /etc/apache2/.htpasswd 41 | Require valid-user 42 | 43 | 44 | 45 | 46 | -------------------------------------------------------------------------------- /templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nhr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nhr -------------------------------------------------------------------------------- /templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nin -------------------------------------------------------------------------------- /templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nog -------------------------------------------------------------------------------- /templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nsd: -------------------------------------------------------------------------------- 1 | chr10 2 | lcl|chr10 3 | -------------------------------------------------------------------------------- /templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nsi: -------------------------------------------------------------------------------- 1 | @4;chr10 -------------------------------------------------------------------------------- /templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nsq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_1/sample_blast_DB_genome.fasta.nsq -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nhr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nhr -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nin -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nog -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nsd: -------------------------------------------------------------------------------- 1 | gene1.10 2 | gene2.11 3 | gene3.12 4 | gene4.13 5 | gene5.14 6 | gene6.15 7 | gene7.16 8 | gene8.17 9 | gene9.18 10 | lcl|gene1.10 11 | lcl|gene2.11 12 | lcl|gene3.12 13 | lcl|gene4.13 14 | lcl|gene5.14 15 | lcl|gene6.15 16 | lcl|gene7.16 17 | lcl|gene8.17 18 | lcl|gene9.18 19 | -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nsi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nsi -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nsq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_nucleotides.fasta.nsq -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.phr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.phr -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.pin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.pin -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.pog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.pog -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.psd: -------------------------------------------------------------------------------- 1 | gene1.10 2 | gene10.19 3 | gene11.110 4 | gene12.111 5 | gene13.112 6 | gene14.113 7 | gene15.114 8 | gene16.115 9 | gene17.116 10 | gene2.11 11 | gene3.12 12 | gene4.13 13 | gene5.14 14 | gene6.15 15 | gene7.16 16 | gene8.17 17 | gene9.18 18 | lcl|gene1.10 19 | lcl|gene10.19 20 | lcl|gene11.110 21 | lcl|gene12.111 22 | lcl|gene13.112 23 | lcl|gene14.113 24 | lcl|gene15.114 25 | lcl|gene16.115 26 | lcl|gene17.116 27 | lcl|gene2.11 28 | lcl|gene3.12 29 | lcl|gene4.13 30 | lcl|gene5.14 31 | lcl|gene6.15 32 | lcl|gene7.16 33 | lcl|gene8.17 34 | lcl|gene9.18 35 | -------------------------------------------------------------------------------- /templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.psi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/blast_dbs/category_2/sample_blast_DB_proteins.fasta.psi -------------------------------------------------------------------------------- /templates/configuration_path.php: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /templates/db_example_annotations/annotation_example_SwissProt.txt: -------------------------------------------------------------------------------- 1 | gene1.1 Q9C5UO Histidine kinase 4 2 | gene2.1 Q9C5U1 Histidine kinase 3 3 | gene3.1 Q9C5U2 Histidine kinase 2 4 | -------------------------------------------------------------------------------- /templates/db_example_annotations/annotation_example_TAIR10.txt: -------------------------------------------------------------------------------- 1 | gene1.1 AT2G01830 Histidine kinase: cytokinin-binding receptor that transduces cytokinin signals across the plasma membrane 2 | gene2.1 AT1G27320 Encodes a histidine kinases, a cytokinin receptor that controls cytokinin-mediated leaf longevity through a specific phosphorylation of the response regulator, ARR2. The mRNA is cell-to-cell mobile 3 | gene3.1 AT5G35750 Encodes histidine kinase AHK2 -------------------------------------------------------------------------------- /templates/db_example_annotations/gene_list.txt: -------------------------------------------------------------------------------- 1 | gene1.1 2 | gene2.1 3 | gene3.1 4 | gene4.1 5 | gene5.1 6 | gene6.1 7 | gene7.1 8 | gene8.1 9 | gene9.1 10 | gene10.1 11 | gene11.1 12 | gene12.1 13 | gene13.1 14 | gene14.1 15 | gene15.1 16 | gene16.1 17 | gene17.1 18 | gene18.1 19 | gene19.1 20 | gene20.1 21 | -------------------------------------------------------------------------------- /templates/downloads/Homo sapiens/Annotations/gene_annotations.txt.gz: -------------------------------------------------------------------------------- 1 | Hello World! -------------------------------------------------------------------------------- /templates/downloads/Homo sapiens/Sequences/Homo_sapiens_v1.0_CDS.fasta.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/downloads/Homo sapiens/Sequences/Homo_sapiens_v1.0_CDS.fasta.gz -------------------------------------------------------------------------------- /templates/downloads/Homo sapiens/Sequences/Homo_sapiens_v1.0_PEP.fasta.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/downloads/Homo sapiens/Sequences/Homo_sapiens_v1.0_PEP.fasta.gz -------------------------------------------------------------------------------- /templates/downloads/Homo sapiens/Sequences/Homo_sapiens_v1.0_cDNA.fasta.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/downloads/Homo sapiens/Sequences/Homo_sapiens_v1.0_cDNA.fasta.gz -------------------------------------------------------------------------------- /templates/downloads/Homo sapiens/Sequences/Homo_sapiens_v1.0_genome.fasta.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/downloads/Homo sapiens/Sequences/Homo_sapiens_v1.0_genome.fasta.gz -------------------------------------------------------------------------------- /templates/downloads/Species species 1/Annotations/gene_annotations.txt: -------------------------------------------------------------------------------- 1 | Hello World! -------------------------------------------------------------------------------- /templates/downloads/Species species 1/Sequences/Species_v1.0_CDS.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/downloads/Species species 1/Sequences/Species_v1.0_CDS.fasta -------------------------------------------------------------------------------- /templates/downloads/Species species 1/Sequences/Species_v1.0_PEP.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/downloads/Species species 1/Sequences/Species_v1.0_PEP.fasta -------------------------------------------------------------------------------- /templates/downloads/Species species 1/Sequences/Species_v1.0_cDNA.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/templates/downloads/Species species 1/Sequences/Species_v1.0_cDNA.fasta 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-------------------------------------------------------------------------------- 1 |

    2 | This is a template to write your own about us page. 3 | Please, follow the instructions to create your own custom_text folder and include the path in the configuration file. 4 |

    5 |

    6 | Lorem ipsum dolor sit amet consectetur adipiscing elit mus nisi vel risus semper sagittis vitae, 7 | luctus platea quisque cum nascetur sem ligula leo magnis cursus cubilia pulvinar. 8 | Habitasse praesent platea nunc pharetra laoreet etiam congue proin, nostra vehicula nec quis iaculis molestie integer diam viverra, 9 | primis nullam gravida massa tempor curae metus. Vitae vivamus nascetur eros mus viverra nostra fames sagittis faucibus donec, 10 | cubilia interdum volutpat augue nisl libero fermentum proin quisque, mollis erat facilisi posuere rutrum luctus quis imperdiet pretium. 11 |

    12 |

    13 | Risus sollicitudin facilisis integer luctus hendrerit aliquet natoque senectus suspendisse, 14 | parturient facilisi laoreet tempor hac cum mi egestas ridiculus, accumsan lacinia inceptos diam commodo per bibendum nullam. 15 | Morbi blandit a suspendisse quis nascetur dignissim tellus, ante ad curabitur leo mauris taciti sollicitudin habitasse, 16 | diam pharetra euismod tristique aliquet nam. Dis nascetur vivamus justo libero platea interdum feugiat tellus, 17 | ad commodo nec etiam volutpat imperdiet viverra, habitasse suspendisse arcu porttitor lacinia iaculis aenean. 18 |

    19 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/custom_cookies.php: -------------------------------------------------------------------------------- 1 |

    2 | This site only uses functional cookies required for login control and needed cookies from third party tools such as JBrowse. 3 | Jbrowse uses cookies to remember your configuration in the genome browser, such as the tracks loaded and the position in the genome. 4 | When using this site you accept the use of the cookies. 5 |

    6 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/custom_footer.php: -------------------------------------------------------------------------------- 1 | "; 12 | } 13 | ?> 14 |
    15 |

    16 | Write your own text here. 17 |

    18 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/custom_pages/other page.php: -------------------------------------------------------------------------------- 1 |

    Other custom page example

    2 | 3 |

    4 | This is a test to show custom pages. 5 |

    6 |

    7 | Lorem ipsum dolor sit amet consectetur adipiscing elit mus nisi vel risus semper sagittis vitae, 8 | luctus platea quisque cum nascetur sem ligula leo magnis cursus cubilia pulvinar. 9 | Habitasse praesent platea nunc pharetra laoreet etiam congue proin, nostra vehicula nec quis iaculis molestie integer diam viverra, 10 | primis nullam gravida massa tempor curae metus. Vitae vivamus nascetur eros mus viverra nostra fames sagittis faucibus donec, 11 | cubilia interdum volutpat augue nisl libero fermentum proin quisque, mollis erat facilisi posuere rutrum luctus quis imperdiet pretium. 12 |

    13 |

    14 | Risus sollicitudin facilisis integer luctus hendrerit aliquet natoque senectus suspendisse, 15 | parturient facilisi laoreet tempor hac cum mi egestas ridiculus, accumsan lacinia inceptos diam commodo per bibendum nullam. 16 | Morbi blandit a suspendisse quis nascetur dignissim tellus, ante ad curabitur leo mauris taciti sollicitudin habitasse, 17 | diam pharetra euismod tristique aliquet nam. Dis nascetur vivamus justo libero platea interdum feugiat tellus, 18 | ad commodo nec etiam volutpat imperdiet viverra, habitasse suspendisse arcu porttitor lacinia iaculis aenean. 19 |

    20 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/custom_pages/row_data.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
    5 |
    6 | 11 | 12 |
    13 |
    14 |

    ".$cols[$title_col]."


    "; 24 | for ($col_count = 0; $col_count <= sizeof($cols); $col_count++) { 25 | if ($header[$col_count]) { 26 | echo "

    ".$header[$col_count].": ".$cols[$col_count]."

    "; 27 | } 28 | } 29 | 30 | } 31 | ?> 32 |
    33 |
    34 | 35 | 36 |
    37 | 38 |
    39 | 40 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/custom_pages/table_menu.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 9 | 10 |
    11 |

    Tables Menu

    12 |
    13 | 29 | 30 |
    31 | 32 |
    33 | 34 | 35 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/custom_toolbar.php: -------------------------------------------------------------------------------- 1 |
  • 2 | More 3 |
    4 | genome 5 | other page 6 | 7 | Table Example 8 | Table Menu 9 | 10 | 11 |
    12 |
    • 13 | 14 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/db_citation.php: -------------------------------------------------------------------------------- 1 |
    2 |
    3 | 4 |

    Please, when using this web site or its data, cite us using the reference:

    5 | 6 |
    7 |
    8 | Last_name, N., Last_name, N., Last_name, N., Last_name, N., Last_name, N. (year). 9 | Title of the publication
    10 | Journal, 1(1), 111
    11 |
    12 |
    13 | 14 |
    15 |
    16 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/expr_datasets/example1_description.php: -------------------------------------------------------------------------------- 1 |

    2 | This is the description of your dataset. 3 | Here you should describe the tissues, stages and experimental conditions, 4 | and you could include a link to the paper where the dataset was published, such as in the next example. 5 | (Fernandez-Pozo and Bombarely) 6 |

    7 | 8 |

    9 | It is also possible to add here some figures or images related to this experiment that could be interesting, 10 | such as photos showing the phenotype for the developmental stages or experimental conditions included in this dataset. 11 |

    12 | img example 13 | img example 14 | img example 15 | img example 16 |
    17 | 18 | -------------------------------------------------------------------------------- /templates/egdb_files/egdb_custom_text/expr_datasets/example2_description.php: -------------------------------------------------------------------------------- 1 |

    2 | This is the description of your dataset. 3 | Here you should describe the tissues, stages and experimental conditions, 4 | and you could include a link to the paper where the dataset was published, such as in the next example. 5 | (Fernandez-Pozo and Bombarely) 6 |

    7 | 8 |

    9 | It is also possible to add here some figures or images related to this experiment that cuold be interesting, 10 | such as photos showing the phenotype for the developmental stages or experimental conditions included in this dataset. 11 |

    12 | img example 13 | img example 14 | img example 15 |
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    2 |

    Species

    3 |
    4 |

    Here, you'll find the information and resources about all the available species.

    5 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/customization/custom_help.json: -------------------------------------------------------------------------------- 1 | { 2 | "search":1, 3 | "blast":2, 4 | "jbrowse":3, 5 | "seq_ext":4, 6 | "annot_ext":5, 7 | "lookup":6, 8 | "enrichment":7, 9 | "gene_expr":8, 10 | "comparator_lookup":9 11 | } 12 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/customization/labs.json: -------------------------------------------------------------------------------- 1 | { 2 | "Lab1": 3 | { 4 | "group_name":"The Wall Lab", 5 | "people": 6 | [ 7 | {"person_name":"Daenerys Targaryen","position":"Principal Investigator","picture":"placeholder1.png","link":"person.php", 8 | "more_info":[ 9 | "phone: 555-123456", 10 | "email: daenerys@got.edu" 11 | ] 12 | }, 13 | {"person_name":"John Snow","position":"Research Assistant","picture":"placeholder2.png","link":"person.php", 14 | "more_info":[ 15 | "phone: 555-123456", 16 | "email: john.snow@got.edu" 17 | ] 18 | }, 19 | {"person_name":"White Walker","position":"PhD Student","picture":"placeholder1.png","link":"person.php", 20 | "more_info":[ 21 | "phone: 555-123456", 22 | "email: white.walker@got.edu" 23 | ] 24 | } 25 | ] 26 | }, 27 | "Lab2": 28 | { 29 | "group_name":"Mordor Lab", 30 | "people": 31 | [ 32 | {"person_name":"Sauron","position":"Principal Investigator","picture":"placeholder2.png","link":"person.php", 33 | "more_info":[ 34 | "phone: 555-123456", 35 | "email: sauron@mordor.edu" 36 | ] 37 | }, 38 | {"person_name":"Uruk hai","position":"Research Assistant","picture":"placeholder1.png","link":"person.php", 39 | "more_info":[ 40 | "phone: 555-123456", 41 | "email: uruk.hai@mordor.edu" 42 | ] 43 | }, 44 | {"person_name":"Orc","position":"PhD Student","picture":"placeholder2.png","link":"person.php", 45 | "more_info":[ 46 | "phone: 555-123456", 47 | "email: orc@mordor.edu" 48 | ] 49 | } 50 | ] 51 | } 52 | } -------------------------------------------------------------------------------- /templates/egdb_files/json_files/customization/logos.json: -------------------------------------------------------------------------------- 1 | { 2 | "logos": 3 | [ 4 | { "image":"logo1.png", 5 | "link":"https://www.google.com/", 6 | "height":"60" 7 | }, 8 | { "image":"logo2.png", 9 | "link":"https://www.google.com/", 10 | "height":"60" 11 | }, 12 | { "image":"logo3.png", 13 | "link":"https://www.google.com/", 14 | "height":"60" 15 | }, 16 | { "image":"logo4.png", 17 | "link":"https://www.google.com/", 18 | "height":"60" 19 | } 20 | ] 21 | } -------------------------------------------------------------------------------- /templates/egdb_files/json_files/customization/species_list.json: -------------------------------------------------------------------------------- 1 | { 2 | "Annona cherimola": 3 | {"card_title":"Annona cherimola", 4 | "card_subtitle":"Cherimoya", 5 | "image":"cherimoya.png", 6 | "public":"1", 7 | "link":"cherimoya.php" 8 | }, 9 | "Mangifera indica": 10 | {"card_title":"Mangifera indica", 11 | "card_subtitle":"Mango", 12 | "image":"mango.png", 13 | "public":"1", 14 | "link":"mango.php" 15 | }, 16 | "Olea europaea": 17 | {"card_title":"Olea europaea", 18 | "card_subtitle":"Olive", 19 | "image":"olive.png", 20 | "public":"1", 21 | "link":"olive.php" 22 | } 23 | } 24 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/tools/annotation_links.json: -------------------------------------------------------------------------------- 1 | { 2 | "TAIR10":"http://www.arabidopsis.org/servlets/TairObject?type=locus&name=query_id", 3 | "Araport11":"http://www.arabidopsis.org/servlets/TairObject?type=locus&name=query_id", 4 | "SwissProt":"http://www.uniprot.org/uniprot/query_id", 5 | "TrEMBL":"http://www.uniprot.org/uniprot/query_id", 6 | "InterPro":"https://www.ebi.ac.uk/interpro/entry/InterPro/query_id", 7 | "NCBI":"https://www.ncbi.nlm.nih.gov/protein/query_id", 8 | "PlantCyc":"https://pmn.plantcyc.org/PLANT/NEW-IMAGE?type=PATHWAY&object=query_id", 9 | "ECs":"https://pmn.plantcyc.org/PLANT/substring-search?type=NIL&object=query_id", 10 | "KEGG":"https://www.genome.jp/entry/query_id", 11 | "GO (BP)": "https://amigo.geneontology.org/amigo/term/query_id", 12 | "GO (MF)": "https://amigo.geneontology.org/amigo/term/query_id", 13 | "GO (CC)": "https://amigo.geneontology.org/amigo/term/query_id" 14 | } 15 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/tools/blast_links.json: -------------------------------------------------------------------------------- 1 | { 2 | "sample_blast_DB_genome.fasta":"/jbrowse/?data=data%2Feasy_gdb_sample&loc={chr}%3A{start}..{end}", 3 | "sample_blast_DB_proteins.fasta":"/easy_gdb/gene.php?name={subject}&annot=example/gene_annotations.txt", 4 | "sample_blast_DB_nucleotides.fasta":"#", 5 | "sample_uniprot.fasta":"https://www.uniprot.org/uniprot/{subject}" 6 | } 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/tools/cartoons_example1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cartoons": 3 | [ 4 | { "img_id":"t1", 5 | "sample":"sample1", 6 | "image":"tissue1.png", 7 | "x":10, 8 | "y":10, 9 | "width":250, 10 | "height":300 11 | }, 12 | { "img_id":"t2", 13 | "sample":"sample2", 14 | "image":"tissue2.png", 15 | "x":10, 16 | "y":10, 17 | "width":250, 18 | "height":300 19 | }, 20 | { "img_id":"t3", 21 | "sample":"sample3", 22 | "image":"tissue3.png", 23 | "x":10, 24 | "y":10, 25 | "width":250, 26 | "height":300 27 | }, 28 | { "img_id":"t4", 29 | "sample":"sample4", 30 | "image":"tissue4.png", 31 | "x":10, 32 | "y":10, 33 | "width":250, 34 | "height":300 35 | } 36 | ] 37 | } 38 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/tools/comparator_link.json: -------------------------------------------------------------------------------- 1 | {"link":"/easy_gdb/gene.php?name=query_id&annot=example/gene_annotations.txt"} 2 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/tools/comparator_lookup.json: -------------------------------------------------------------------------------- 1 | { 2 | "gene1.1":"new_gene1.1", 3 | "gene2.1":"new_gene2.1", 4 | "gene3.1":"new_gene3.1", 5 | "gene4.1":"new_gene4.1", 6 | "gene5.1":"new_gene5.1", 7 | "gene6.1":"new_gene6.1", 8 | "gene7.1":"new_gene7.1", 9 | "gene8.1":"new_gene8.1", 10 | "gene9.1":"new_gene9.1", 11 | "gene10.1":"new_gene10.1", 12 | "gene11.1":"new_gene11.1", 13 | "gene12.1":"new_gene12.1", 14 | "gene13.1":"new_gene13.1", 15 | "gene14.1":"new_gene14.1", 16 | "gene15.1":"new_gene15.1", 17 | "gene16.1":"new_gene16.1", 18 | "gene17.1":"new_gene17.1", 19 | "gene18.1":"new_gene18.1", 20 | "gene19.1":"new_gene19.1", 21 | "gene20.1":"new_gene20.1" 22 | } -------------------------------------------------------------------------------- /templates/egdb_files/json_files/tools/enrichment.json: -------------------------------------------------------------------------------- 1 | { 2 | "A.thaliana": 3 | {"gprofiler_sps" : "athaliana", 4 | "lookup_files": 5 | [ 6 | "Species1_Arabidopsis_Best_hit.txt" 7 | ] 8 | } 9 | } 10 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/tools/expression_info.json: -------------------------------------------------------------------------------- 1 | { 2 | "Example1 - Plant_gene_expression_RPKM.txt": 3 | {"link":"", 4 | "annotation_file":"example/gene_annotations.txt", 5 | "description":"example1_description.php", 6 | "images": 7 | { 8 | "Leaf":"leaf.jpeg", 9 | "Fruit":"fruit.jpeg", 10 | "Root":"root.jpeg", 11 | "Peel":"peel.jpeg", 12 | "Seed":"seed.jpeg", 13 | "Germinating Seed":"germinating_seed.jpeg", 14 | "Darkness":"darkness.jpeg", 15 | "Drought":"drought.jpeg", 16 | "Heat":"heat.jpeg", 17 | "Cold":"cold.jpeg" 18 | } 19 | }, 20 | "Example2 - Organism dataset name.txt": 21 | {"link":"#", 22 | "description":"example2_description.php" 23 | }, 24 | "Example3 - Dataset with cartoons.txt": 25 | { 26 | "link":"", 27 | "annotation_file":"example/gene_annotations.txt", 28 | "cartoons":"cartoons_example1.json", 29 | "expression_colors": 30 | { 31 | "colors":["#c8c8c8","#f0c320","#ff8800","#ff7469","#de2515","#b71005","#0bb4ff","#4c2882"], 32 | "ranges_txt":["<1",">=1",">=2",">=5",">=10",">=50",">=100",">=200"], 33 | "ranges":[[0,0.99],[1,1.99],[2,4.99],[5,9.99],[10,49.99],[50,99.99],[100,199.99],[200,49999.99]] 34 | } 35 | } 36 | 37 | } 38 | -------------------------------------------------------------------------------- /templates/egdb_files/json_files/tools/vcf.json: -------------------------------------------------------------------------------- 1 | { 2 | "gene_names_file":"gene_names.txt", 3 | "gff_file":"gene_models.gff.gz", 4 | "jb_data_folder":"easy_gdb_sample", 5 | "passport_folder":"passport_folder", 6 | "chr_files": 7 | { 8 | "chr1":"chr1.ann.vcf.gz", 9 | "chr2":"chr2.ann.vcf.gz", 10 | "chr3":"chr3.ann.vcf.gz", 11 | "chr4":"chr4.ann.vcf.gz", 12 | "chr5":"chr5.ann.vcf.gz", 13 | "chr6":"chr6.ann.vcf.gz", 14 | "chr7":"chr7.ann.vcf.gz", 15 | "chr8":"chr8.ann.vcf.gz" 16 | } 17 | } -------------------------------------------------------------------------------- /templates/expression_data/Example1_2 - Plant_gene_expression_sample.txt: -------------------------------------------------------------------------------- 1 | Gene ID sample1 sample1 sample1 sample2 sample2 sample2 sample3 sample3 sample3 sample4 sample4 sample4 2 | new_gene1.1 1.11 1.48 1.56 5.17 6.85 5.75 18.5 20.55 21.28 102.72 101.1 101.03 3 | new_gene2.1 271.76 254.72 262.99 57.32 58.49 57.32 2.32 2.42 2.02 525.55 560.75 524.8 4 | new_gene3.1 109.38 126.12 117.03 36.56 41.09 38.45 0.88 0.97 0.59 5.99 5.4 5.95 5 | new_gene4.1 2.28 2.1 2.93 119.21 111.27 126.64 16.04 12.58 17.79 505.55 504.69 501.53 6 | new_gene5.1 1.91 1.39 1.37 17.61 15.69 12.05 56.91 59.96 54.51 135.06 135.64 137 7 | new_gene6.1 74.38 247.32 231.82 62.47 105.34 23.73 46.18 149.33 64.06 73.07 238.76 171.74 8 | new_gene7.1 165.48 115.26 240.63 219.25 78.12 88.22 62.49 245.16 79.34 157.88 245.88 243.56 9 | new_gene8.1 111.24 225.42 174.8 56.34 207.77 64.41 12.19 76.11 159.94 131 247.18 34.99 10 | new_gene9.1 62.66 164.92 133.69 96.39 27.51 90.18 194.41 130.59 65.01 219.1 145.74 43.09 11 | new_gene10.1 68.34 222.33 215.6 211.64 162.9 47.42 229.27 68.14 112.02 4.78 145.37 138.21 12 | new_gene11.1 181.43 138.03 237.82 11.47 231.13 85.96 224.33 219.86 80.98 176.4 65.52 215.86 13 | new_gene12.1 85.82 195.26 245.01 111.39 215.14 7.53 235.21 62.35 184.86 189.44 218.98 198.35 14 | new_gene13.1 240.72 76.31 229.27 80.85 162.41 139.83 25.35 238.34 18.49 242.17 170.64 52.47 15 | new_gene14.1 242.38 155.47 215.42 13.77 39.77 139.07 89.11 13.53 41.22 142.85 52.68 82.66 16 | new_gene15.1 58.96 182.43 156.99 161.61 34.03 181.52 185.09 155.64 74.29 59.71 204.13 154.11 17 | new_gene16.1 173.35 175.27 148.28 94.1 213.69 77.17 10.53 239.02 183.08 217.13 90.53 151.29 18 | new_gene17.1 7.76 141.05 134.9 242.73 128.31 226.71 129.03 69.52 76.15 63.7 78.37 136.69 19 | new_gene18.1 181.86 136.31 17.77 248.03 243.14 163.47 187.44 234.99 52.43 71.95 125.08 159.61 20 | new_gene19.1 13.95 78.59 26.58 187.51 22.23 46.31 155.03 249.62 225.41 221.73 127.98 21.51 21 | new_gene20.1 36.21 56.23 51.28 19.23 94.23 203.47 25.28 112.39 134.28 63.3 121.34 144.83 -------------------------------------------------------------------------------- /templates/jbrowse_example_data/gene_models.gff: -------------------------------------------------------------------------------- 1 | ##gff-version 3 2 | Chr1 easyGDB gene 1250 3000 . + . ID=gene1 3 | Chr1 easyGDB mRNA 1250 3000 . + . ID=gene1.1;Name=gene1.1;Parent=gene1;Note="Histidine kinase 4" 4 | Chr1 easyGDB five_prime_UTR 1250 250 . + . Parent=gene1.1 5 | Chr1 easyGDB exon 1250 800 . + . Parent=gene1.1 6 | Chr1 easyGDB CDS 1251 800 . + . Parent=gene1.1 7 | Chr1 easyGDB exon 1500 2000 . + . Parent=gene1.1 8 | Chr1 easyGDB CDS 1500 2000 . + . Parent=gene1.1 9 | Chr1 easyGDB exon 2500 2800 . + . Parent=gene1.1 10 | Chr1 easyGDB three_prime_UTR 2800 3000 . + . Parent=gene1.1 11 | Chr1 easyGDB gene 3250 6200 . - . ID=gene2 12 | Chr1 easyGDB mRNA 3250 6200 . - . ID=gene2.1;Name=gene2.1;Parent=gene2;Note="Histidine kinase 3" 13 | Chr1 easyGDB three_prime_UTR 3250 3550 . - . Parent=gene2.1 14 | Chr1 easyGDB exon 3250 3950 . - . Parent=gene2.1 15 | Chr1 easyGDB CDS 3551 3950 . - . Parent=gene2.1 16 | Chr1 easyGDB exon 4100 4900 . - . Parent=gene2.1 17 | Chr1 easyGDB CDS 4100 4900 . - . Parent=gene2.1 18 | Chr1 easyGDB exon 5400 6200 . - . Parent=gene2.1 19 | Chr1 easyGDB CDS 5400 5799 . - . Parent=gene2.1 20 | Chr1 easyGDB five_prime_UTR 5800 6200 . - . Parent=gene2.1 21 | Chr1 easyGDB gene 7100 10000 . + . ID=gene3 22 | Chr1 easyGDB mRNA 7100 10000 . + . ID=gene3.1;Name=gene3.1;Parent=gene3;Note="Histidine kinase 2" 23 | Chr1 easyGDB five_prime_UTR 7100 7250 . + . Parent=gene3.1 24 | Chr1 easyGDB exon 7100 7800 . + . Parent=gene3.1 25 | Chr1 easyGDB CDS 7251 7800 . + . Parent=gene3.1 26 | Chr1 easyGDB exon 8500 9000 . + . Parent=gene3.1 27 | Chr1 easyGDB CDS 8500 9000 . + . Parent=gene3.1 28 | Chr1 easyGDB exon 9500 10000 . + . Parent=gene3.1 29 | Chr1 easyGDB exon 9500 9799 . + . Parent=gene3.1 30 | Chr1 easyGDB three_prime_UTR 9800 10000 . + . Parent=gene3.1 31 | -------------------------------------------------------------------------------- /templates/jbrowse_example_data/trackList.json: -------------------------------------------------------------------------------- 1 | { 2 | "formatVersion" : 1, 3 | "names" : { 4 | "type" : "Hash", 5 | "url" : "names/" 6 | }, 7 | "tracks" : [ 8 | { 9 | "category" : "Reference sequence", 10 | "chunkSize" : 20000, 11 | "key" : "Reference sequence", 12 | "label" : "DNA", 13 | "seqType" : "dna", 14 | "storeClass" : "JBrowse/Store/Sequence/StaticChunked", 15 | "type" : "SequenceTrack", 16 | "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-" 17 | }, 18 | { 19 | "category" : "02 Annotations", 20 | "compress" : 0, 21 | "key" : "EasyGDB gene models", 22 | "label" : "egdb_gene_models", 23 | "onClick" : { 24 | "action" : "newWindow", 25 | "label" : "Go to gene view", 26 | "url" : "/easy_gdb/gene.php?name={id}" 27 | }, 28 | "storeClass" : "JBrowse/Store/SeqFeature/NCList", 29 | "style" : { 30 | "className" : "feature" 31 | }, 32 | "trackType" : "CanvasFeatures", 33 | "type" : "CanvasFeatures", 34 | "urlTemplate" : "tracks/egdb_gene_models/{refseq}/trackData.json" 35 | } 36 | ] 37 | } 38 | -------------------------------------------------------------------------------- /templates/jbrowse_example_data/tracks.conf: -------------------------------------------------------------------------------- 1 | [general] 2 | dataset_id = easy_gdb_sample 3 | 4 | -------------------------------------------------------------------------------- /templates/lookup/Species1_Arabidopsis_Best_hit.txt: -------------------------------------------------------------------------------- 1 | gene1.1 AT3G02850 2 | gene2.1 AT5G12210 3 | gene3.1 AT3G61650 4 | gene4.1 AT1G01780 5 | gene5.1 AT4G38510 6 | gene6.1 AT4G13930 7 | gene7.1 AT5G44520 8 | gene8.1 AT1G48635 9 | gene9.1 AT4G12920 10 | gene10.1 AT4G30530 11 | gene11.1 AT3G23090 12 | gene12.1 AT4G34090 13 | gene13.1 AT3G28630 14 | gene14.1 AT3G57200 15 | gene15.1 AT5G67470 16 | gene16.1 AT1G36370 17 | gene17.1 AT1G23310 18 | gene18.1 AT3G05520 19 | gene19.1 AT4G13890 20 | gene20.1 AT1G07510 21 | gene21.1 AT2G05830 22 | gene22.1 AT5G24090 23 | gene23.1 AT2G35260 24 | gene24.1 AT2G37620 25 | gene25.1 AT3G46520 26 | -------------------------------------------------------------------------------- /templates/passport/example/Species_1/passport.json: -------------------------------------------------------------------------------- 1 | { 2 | "passport_file":"sp1_passport.txt", 3 | "acc_link":"ACC Name", 4 | "phenotype_files":["Leaf_descriptors.txt", "Flower_descriptors.txt", "Fruit_descriptors.txt"], 5 | "map_columns":[2,5,10,11], 6 | "map_markers":[], 7 | "sp_name":"Species_1" 8 | } -------------------------------------------------------------------------------- /templates/passport/example/Species_1/sp1_passport.txt: -------------------------------------------------------------------------------- 1 | ID ACC Name Species Germplasm type Country Country code Research Center Biological status of accession Collecting/acquisition source Latitude Longitude 2 | ID1 ACC1 Annona cherimola Tree Spain ESP easyGDB Clonal selection Orchad 36.73555555555550 -3.689722222222220 3 | ID2 ACC2 Annona cherimola Tree Spain ESP easyGDB Clonal selection Orchad 36.73555555555550 -3.689722222222220 4 | ID3 ACC3 Annona cherimola Tree Unknown easyGDB Clonal selection Orchad 36.73555555555550 -3.689722222222220 5 | ID4 ACC4 Annona cherimola Tree Unknown easyGDB Clonal selection Orchad 36.73555555555550 -3.689722222222220 6 | ID5 ACC5 Annona cherimola Tree Unknown easyGDB Clonal selection Orchad 36.73555555555550 -3.689722222222220 7 | ID6 ACC6 Annona cherimola Tree Unknown easyGDB Clonal selection Orchad 36.73555555555550 -3.689722222222220 8 | ID7 ACC7 Annona cherimola Tree Peru PER easyGDB Breeding/research material Backyard 9 | ID8 ACC8 Annona cherimola Tree Chile CHL easyGDB Clonal selection Orchad 10 | ID9 ACC9 Annona cherimola Tree Unknown easyGDB Clonal selection Orchad 11 | ID10 ACC10 Annona cherimola Tree Chile CHL easyGDB Clonal selection Orchad 12 | ID11 ACC11 Annona cherimola Tree Peru PER easyGDB Breeding/research material Backyard 13 | ID12 ACC12 Annona cherimola Tree United States of America USA easyGDB Clonal selection Orchad 14 | ID13 ACC13 Annona cherimola Tree United States of America USA easyGDB Clonal selection Orchad 15 | ID14 ACC14 Annona cherimola Tree Mexico MEX easyGDB Clonal selection Orchad 16 | ID15 ACC15 Annona cherimola Tree United States of America USA easyGDB Clonal selection Orchad 17 | ID16 ACC16 Annona cherimola Tree Chile CHL easyGDB Clonal selection Orchad -29.90777777777770 -71.25416666666660 18 | ID17 ACC17 Annona cherimola Tree Peru PER easyGDB Breeding/research material Backyard -10.125 -77.075 19 | ID18 ACC18 Annona cherimola Tree Peru PER easyGDB Breeding/research material Backyard -10.125 -77.075 20 | ID19 ACC19 Annona cherimola Tree Peru PER easyGDB Breeding/research material Backyard -10.125 -77.075 21 | ID20 ACC20 Annona cherimola Tree Peru PER easyGDB Breeding/research material Backyard -9.258333333333330 -77.025 -------------------------------------------------------------------------------- /templates/passport/example/Species_2/featured_descriptors.json: -------------------------------------------------------------------------------- 1 | { 2 | "Inflorescence_descriptors.txt": 3 | [ 4 | "Flowering type" 5 | ], 6 | "Ripe_fruit_descriptors.txt": 7 | [ 8 | "Color", 9 | "Thickness skin", 10 | "Consistency", 11 | "Adherence skin/flesh", 12 | "Main color flesh" 13 | ] 14 | } -------------------------------------------------------------------------------- /templates/passport/example/Species_2/passport.json: -------------------------------------------------------------------------------- 1 | { 2 | "passport_file":"sp2_passport.txt", 3 | "acc_link":"ACC Name", 4 | "phenotype_files":["Leaf_descriptors.txt", "Inflorescence_descriptors.txt", "Mature_fruit_descriptors.txt", "Ripe_fruit_descriptors.txt"], 5 | "phenotype_imgs":"sp2_phenotype_imgs.json", 6 | "img_src_msg":"

    The images used in the Phenotype descriptors come from Manual gráfico para la descripción varietal del aguacate. (Sagarpa). Using UPOV Database (Genie) for descriptors.

    ", 7 | "map_columns":[2,6,11,12], 8 | "map_markers":[], 9 | "phenotype_file_marker_trait":"", 10 | "marker_column":"", 11 | "sp_name":"Species_2", 12 | "convert_to_cathegoric":"convert_numeric_to_cathegoric.json", 13 | "translator":"translator.json", 14 | "featured_descriptors":"featured_descriptors.json" 15 | } -------------------------------------------------------------------------------- /templates/passport/example/Species_2/sp2_passport.txt: -------------------------------------------------------------------------------- 1 | ID ACC Name Species Germplasm type Date Country Country code Research Center Biological status of ACC Collecting/acquisition source Latitude Longitude 2 | ID1 ACC1 Persea americana Tree 2024 South Africa ZAF easyGDB Clonal selection Cultivated habitat 3 | ID2 ACC2 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 4 | ID3 ACC3 Persea americana Tree 2024 Mexico MEX easyGDB Clonal selection Cultivated habitat 5 | ID4 ACC4 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 6 | ID5 ACC5 Persea americana Tree 2024 Unknown easyGDB Clonal selection Cultivated habitat 7 | ID6 ACC6 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 8 | ID7 ACC7 Persea americana Tree 2024 Israel ISR easyGDB Clonal selection Cultivated habitat 9 | ID8 ACC8 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 10 | ID9 ACC9 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 11 | ID10 ACC10 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 12 | ID1 ACC11 Persea americana Tree 2024 Colombia COL easyGDB Clonal selection Cultivated habitat 13 | ID2 ACC12 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Farm 14 | ID3 ACC13 Persea americana Tree 2024 Mexico MEX easyGDB Clonal selection Farm 15 | ID4 ACC14 Persea americana Tree 2024 Venezuela VEN easyGDB Clonal selection Cultivated habitat 16 | ID5 ACC15 Persea americana Tree 2024 Israel ISR easyGDB Clonal selection Cultivated habitat 17 | ID6 ACC16 Persea americana Tree 2024 Mexico MEX easyGDB Clonal selection Cultivated habitat 18 | ID7 ACC17 Persea americana Tree 2024 Israel ISR easyGDB Clonal selection Cultivated habitat 19 | ID8 ACC18 Persea americana Tree 2024 Spain ESP easyGDB Clonal selection Cultivated habitat 20 | ID9 ACC19 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 21 | ID10 ACC20 Persea americana Tree 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 22 | ID1 ACC21 Persea americana Tree 2024 South Africa ZAF easyGDB Clonal selection Cultivated habitat -------------------------------------------------------------------------------- /templates/passport/example/Species_3/Phenotype_descriptors.txt: -------------------------------------------------------------------------------- 1 | Date ACC Name Length blade Width blade Ratio length/width Shape blade Twisting blade Shape base blade Shape apex blade Length inflorescence Diameter inflorescence Ratio length/diameter Primary branches inflorescence Length fruit Width fruit Ratio length/width fruit Shape cross fruit Stalk cavity fruit Neck fruit Color skin fruit Speckling skin fruit Adherence skin to flesh fruit Main color flesh fruit 2 | 3 mar 2016 ACC4 18.8 5.3 3.547169811 oblong absent acute acuminate 25 16 1.5625 21 95.98 63.8 1.504388715 broad elliptic medium absent orange weak weak medium orange 3 | 3 mar 2016 ACC6 24.3 7.1 3.422535211 oblong absent obtuse acuminate 29 10 2.9 21 210.13 160.31 1.310772878 broad elliptic absent absent orange and red strong medium medium orange 4 | 4 mar 2016 ACC5 20.4 6.1 3.344262295 ovate absent acute acute 36 15 2.4 17 red absent weak light orange 5 | 4 mar 2016 ACC7 17.8 4.5 3.955555556 oblong absent acute acuminate 25 12 2.083333333 23 117.76 84.8 1.388679245 broad elliptic medium absent green 6 | 27 apr 2016 ACC10 21.3 5.6 3.803571429 ovate absent acute acuminate 30 21 1.428571429 19 142.1 96.63 1.470557798 broad elliptic shallow absent yellow and red absent strong medium orange 7 | 19 feb 2016 ACC11 18.2 7 2.6 elliptic absent acute acuminate 15 9 1.666666667 20 103.38 82.03 1.260270633 broad elliptic medium absent yellow weak weak medium yellow 8 | 16 mar 2016 ACC8 19.2 5 3.84 oblong absent obtuse acute 36 15 2.4 22 108.79 95.72 1.136544087 broad elliptic absent absent yellow absent strong medium orange 9 | 08 mar 2016 ACC9 19.5 4.3 4.534883721 ovate absent acute acuminate 23 9 2.555555556 9 180 67.61 2.662328058 circular absent absent orange and red weak weak medium orange 10 | 01 apr 2016 ACC1 18.8 5.1 3.68627451 ovate absent acute acute 30 20 1.5 22 143.51 87.26 1.644625258 medium elliptic absent absent purple medium strong medium orange 11 | 14 apr 2016 ACC12 14 3.5 4 ovate absent acute acute 18 12 1.5 20 107.83 93.47 1.153632181 circular medium absent purple weak medium medium orange 12 | 01 apr 2016 ACC2 25.6 5.5 4.654545455 ovate absent acute acute 28 14 2 30 127.28 88.29 1.441612867 circular absent absent red weak medium medium orange -------------------------------------------------------------------------------- /templates/passport/example/Species_3/passport.json: -------------------------------------------------------------------------------- 1 | { 2 | "passport_file":"sp3_passport.txt", 3 | "acc_link":"ACC Name", 4 | "phenotype_files":["Phenotype_descriptors.txt"], 5 | "phenotype_imgs":"sp3_phenotype_imgs.json", 6 | "img_src_msg":"

    The images used in the Phenotype descriptors come from UPOV Database (Genie).

    ", 7 | "map_columns":[2,6,11,12], 8 | "map_markers":["green","yellow_green","green_and_yellow","yellow","yellow_orange","yellow_and_orange","orange","yellow_and_red","orange_and_red","red","orange_and_purple","red_and_purple","purple"], 9 | "phenotype_file_marker_trait":"Phenotype_descriptors.txt", 10 | "marker_acc_col":"2", 11 | "marker_column":"20", 12 | "sp_name":"Species_3", 13 | "convert_to_cathegoric":"convert_numeric_to_cathegoric.json", 14 | "translator":"translator.json" 15 | } -------------------------------------------------------------------------------- /templates/passport/example/Species_3/sp3_passport.txt: -------------------------------------------------------------------------------- 1 | ID ACC Name Species Germplasm type Date Country Country code Research Center Biological status of ACC Collecting/acquisition source Latitude Longitude 2 | ID1 ACC1 Mangifera indica Tree 01 Jan 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 3 | ID2 ACC2 Mangifera indica Tree 02 Jan 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 4 | ID3 ACC3 Mangifera indica Tree 03 Jan 2024 Israel ISR easyGDB Clonal selection Cultivated habitat 5 | ID4 ACC4 Mangifera indica Tree 04 Jan 2024 Mexico MEX easyGDB Clonal selection Cultivated habitat 6 | ID5 ACC5 Mangifera indica Tree 05 Jan 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 7 | ID6 ACC6 Mangifera indica Tree 06 Jan 2024 Israel ISR easyGDB Clonal selection Farm or cultivated habitat 8 | ID7 ACC7 Mangifera indica Tree 07 Jan 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 9 | ID8 ACC8 Mangifera indica Tree 08 Jan 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 10 | ID9 ACC9 Mangifera indica Tree 09 Jan 2024 Thailand THA easyGDB Clonal selection Cultivated habitat 11 | ID10 ACC10 Mangifera indica Tree 10 Jan 2024 United States of America USA easyGDB Clonal selection Cultivated habitat 12 | ID11 ACC11 Mangifera indica Tree 11 Jan 2024 Australia AUS easyGDB Clonal selection Cultivated habitat 13 | ID12 ACC12 Mangifera indica Tree 12 Jan 2024 Unknown easyGDB Clonal selection Cultivated habitat -------------------------------------------------------------------------------- /templates/passport/example/Species_3/sp3_phenotype_imgs.json: -------------------------------------------------------------------------------- 1 | { 2 | "Phenotype_descriptors.txt": 3 | { 4 | "Primary branches inflorescence": 5 | { 6 | "img_name":"upov_inflorescence_number_primary_branches_help.png", 7 | "options":["few","medium","many"] 8 | }, 9 | "Shape blade": 10 | { 11 | "img_name":"upov_leaf_blade_shape_value.png", 12 | "options":["ovate","elliptic","oblong"] 13 | }, 14 | "Twisting blade": 15 | { 16 | "img_name":"upov_leaf_blade_twisting_value.png", 17 | "options":["absent","present"] 18 | }, 19 | "Shape base blade": 20 | { 21 | "img_name":"upov_leaf_blade_shape_base_value.png", 22 | "options":["acute","obtuse","rounded"] 23 | }, 24 | "Shape apex blade": 25 | { 26 | "img_name":"upov_leaf_blade_shape_apex_value.png", 27 | "options":["attenuate","acuminate","acute"] 28 | }, 29 | "Ratio length/width fruit": 30 | { 31 | "img_name":"upov_mature_fruit_ratio_help.png", 32 | "options":["very_small","small","medium","large"] 33 | }, 34 | "Shape cross fruit": 35 | { 36 | "img_name":"upov_mature_fruit_shape_cross_section_value.png", 37 | "options":["medium_elliptic","broad_elliptic","circular"] 38 | }, 39 | "Stalk cavity fruit": 40 | { 41 | "img_name":"upov_mature_fruit_stalk_cavity_value.png", 42 | "options":["absent","shallow","medium","deep"] 43 | }, 44 | "Neck fruit": 45 | { 46 | "img_name":"upov_mature_fruit_presence_neck_value.png", 47 | "options":["absent","present"] 48 | } 49 | } 50 | } -------------------------------------------------------------------------------- /templates/passport/example/germplasm_list.json: -------------------------------------------------------------------------------- 1 | { 2 | "Species_1": 3 | { 4 | "Annona cherimola": 5 | {"sps_name":"Annona cherimola", 6 | "common_name":"Cherimoya", 7 | "image":"sp1.png", 8 | "public":"1", 9 | "link":"02_pass_file_to_datatable.php?dir_name=Species_1" 10 | } 11 | }, 12 | "Species_2": 13 | { 14 | "Persea americana": 15 | {"sps_name":"Persea americana", 16 | "common_name":"Avocado", 17 | "image":"sp2.png", 18 | "public":"1", 19 | "link":"02_pass_file_to_datatable.php?dir_name=Species_2" 20 | } 21 | }, 22 | "Species_3": 23 | { 24 | "Mangifera indica": 25 | {"sps_name":"Mangifera indica", 26 | "common_name":"Mango", 27 | "image":"sp3.png", 28 | "public":"1", 29 | "link":"02_pass_file_to_datatable.php?dir_name=Species_3" 30 | } 31 | } 32 | } -------------------------------------------------------------------------------- /tools/blast/blastdbcmd.php: -------------------------------------------------------------------------------- 1 | 44 | -------------------------------------------------------------------------------- /tools/blast/blastdbcmd_multiple.php: -------------------------------------------------------------------------------- 1 | isFile()) { 20 | $extension = pathinfo($file->getFilename(), PATHINFO_EXTENSION); 21 | if (in_array($extension, $allowedExtensions)) { 22 | $baseName = $file->getFilename(); 23 | if ($baseName === $dbPath) { 24 | return $file->getPathname(); 25 | } 26 | } 27 | } 28 | } 29 | return null; 30 | } 31 | 32 | 33 | // BLASTDBCMD 34 | function getFastaFile($gids, $dbPath) { 35 | exec("blastdbcmd -db {$dbPath} -entry " . escapeshellarg(implode(",", $gids)) . " | sed 's/lcl|//'", $ret); 36 | return implode("\n", $ret); 37 | } 38 | 39 | 40 | // POST 41 | if (isset($_POST["gids"]) && isset($_POST["selected_dbs"])) { 42 | $gids = array_map('trim', explode("\n", $_POST["gids"])); 43 | $databases = explode(",", $_POST["selected_dbs"]); 44 | header('Content-Type: application/octet-stream'); 45 | 46 | // CHANGE NAME 47 | $filename="$dbTitle" . "_" . date("Y-m-d_His") . ".fasta"; 48 | header("Content-Disposition: attachment;filename={$filename}"); 49 | $results = []; 50 | 51 | // FUNCTION 52 | foreach ($databases as $dbPath) { 53 | $resolvedPath = findPath($dbPath, $baseDir); 54 | $resolvedPath = preg_replace('/\.(nhr|phr)$/i', '', $resolvedPath); 55 | if (!empty($resolvedPath)) { 56 | $sequences = getFastaFile($gids, $resolvedPath); 57 | if (!empty($sequences)) { 58 | $results[] = $sequences; 59 | ob_clean(); 60 | flush(); 61 | } 62 | } 63 | } 64 | echo implode("\n\n", $results); 65 | exit; 66 | } 67 | 68 | 69 | ?> -------------------------------------------------------------------------------- /tools/blast/blastdbcmd_single.php: -------------------------------------------------------------------------------- 1 | 44 | -------------------------------------------------------------------------------- /tools/blast/get_dbs.php: -------------------------------------------------------------------------------- 1 | $blast_db"; 25 | } 26 | 27 | } 28 | } 29 | } 30 | } 31 | 32 | // } 33 | ?> 34 | -------------------------------------------------------------------------------- /tools/blast/loading_blast.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 13 | 14 |
    15 | 18 |

    Processing your request. Please wait...

    19 |
    20 | 21 | 22 | 23 | 34 | 35 | 36 | 37 | 52 | 53 | 59 | -------------------------------------------------------------------------------- /tools/coexpression/ajax_get_names_array.php: -------------------------------------------------------------------------------- 1 | 22 | -------------------------------------------------------------------------------- /tools/coexpression/coex_modal.php: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/common_functions.php: -------------------------------------------------------------------------------- 1 | ]+/','',$data); 7 | $data = htmlspecialchars($data); 8 | 9 | return $data; 10 | } 11 | 12 | function test_input2($data) { 13 | $data = preg_replace('/[\<\>\t\r\;]+/', '', $data); 14 | $data = htmlspecialchars($data); 15 | if (preg_match('/\s+/', $data)) { 16 | $data_array = explode(' ', $data, 99); 17 | foreach ($data_array as $key => &$value) { 18 | if (strlen($value) < 3) { 19 | unset($data_array[$key]); 20 | } 21 | } 22 | $data = implode(' ',$data_array); 23 | } 24 | $data = stripslashes($data); 25 | return $data; 26 | } 27 | 28 | function get_dir_and_files($dir_name) { 29 | $file_array = array(); 30 | 31 | $pattern='/^\./'; 32 | if (is_dir($dir_name)){ 33 | if ($dh = opendir($dir_name)){ 34 | while (($file_name = readdir($dh)) !== false){ 35 | $is_not_file = preg_match($pattern, $file_name, $match); 36 | if (!$is_not_file) { 37 | // echo $file_name."
    "; 38 | array_push($file_array,$file_name); 39 | } 40 | } 41 | } 42 | } 43 | 44 | rsort($file_array); 45 | return $file_array; 46 | } 47 | 48 | 49 | ?> 50 | 51 | -------------------------------------------------------------------------------- /tools/expression/01_expr_check_dataset_description.php: -------------------------------------------------------------------------------- 1 | $dataset_name"; 9 | } 10 | 11 | // if ( file_exists("$expression_path/expression_info.json") ) { 12 | // $annot_json_file = file_get_contents("$expression_path/expression_info.json"); 13 | // $annot_hash = json_decode($annot_json_file, true); 14 | if ($annot_hash) { 15 | 16 | if ($annot_hash[$dataset_name_ori]["description"]) { 17 | 18 | $desc_file = $annot_hash[$dataset_name_ori]["description"]; 19 | 20 | if ( file_exists("$custom_text_path/expr_datasets/$desc_file") ) { 21 | 22 | // echo "

    $dataset_name

    "; 23 | echo "

    $r_key

    "; 24 | $description_files_found=true; // the dataset information files exist 25 | } 26 | // else { 27 | // echo "

    $dataset_name

    "; 28 | // } 29 | } 30 | 31 | if ($annot_hash[$dataset_name_ori]["images"]) { 32 | $expr_img_array = $annot_hash[$dataset_name_ori]["images"]; 33 | } 34 | 35 | // print("
    ".print_r($expr_img_array,true)."
    "); 36 | 37 | } 38 | 39 | ?> -------------------------------------------------------------------------------- /tools/expression/01_expr_load_description.php: -------------------------------------------------------------------------------- 1 | '; 7 | echo ' Description dataset'; 8 | echo '
    '; 9 | 10 | echo '
    '; 11 | include("$custom_text_path/expr_datasets/$desc_file"); 12 | echo "
    "; 13 | 14 | } 15 | ?> -------------------------------------------------------------------------------- /tools/expression/03_expr_load_avg_table_html.php: -------------------------------------------------------------------------------- 1 | 2 |
    3 | Average values 4 |
    5 | 6 |
    7 | 8 |
    9 | 10 | 11 | 12 | 17 | 18 | 19 | 20 |
    21 | 22 | 35 | 36 | 37 | 38 | 52 | 53 | -------------------------------------------------------------------------------- /tools/expression/03_expr_load_heatmap_html.php: -------------------------------------------------------------------------------- 1 | 2 | 3 |
    4 | 5 |
    6 | Heatmap 7 |
    8 | 9 |
    10 | 11 |
    12 | 13 | 14 | 15 | 16 |
    17 | 18 |
    19 |
    20 |
    21 | -------------------------------------------------------------------------------- /tools/expression/03_expr_load_lines_html.php: -------------------------------------------------------------------------------- 1 | 2 |
    3 | 4 |
    5 | Lines 6 |
    7 | 8 |
    9 | 10 | 11 |
    12 | 13 | 14 | 15 |
    16 | 17 |
    18 | 19 | 20 | 21 |
    22 |
    23 | -------------------------------------------------------------------------------- /tools/expression/03_expr_load_replicates_html.php: -------------------------------------------------------------------------------- 1 | 2 |
    3 | 4 |
    5 | Replicates 6 |
    7 | 8 |
    9 | 10 |
    11 |
    12 | 13 | 20 |
    21 |
    22 |
    23 | 24 |
    25 |
    26 | -------------------------------------------------------------------------------- /tools/expression/ajax_get_names_array.php: -------------------------------------------------------------------------------- 1 | 25 | -------------------------------------------------------------------------------- /tools/expression/card_pattern.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/tools/expression/card_pattern.png -------------------------------------------------------------------------------- /tools/expression/expr_placeholder.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/noefp/easy_gdb/4c904e7795e282a7756f9d0ef173000f14fc068e/tools/expression/expr_placeholder.jpeg -------------------------------------------------------------------------------- /tools/expression/expression_menu.php: -------------------------------------------------------------------------------- 1 | 2 |
    3 |

    Expression Datasets

    4 |
    5 | $r_value) { 12 | if ($annot_hash[$r_key]["description"]) { 13 | 14 | $desc_file = $annot_hash[$r_key]["description"]; 15 | if ( file_exists("$custom_text_path/expr_datasets/$desc_file") ) { 16 | $data_set_name = preg_replace('/\.[a-z]{3}$/',"",$r_key); 17 | $data_set_name = str_replace("_"," ",$data_set_name); 18 | 19 | echo "

    $data_set_name

    "; 20 | include("$custom_text_path/expr_datasets/$desc_file"); 21 | echo"
    "; 22 | echo"
    "; 23 | } 24 | } 25 | } 26 | } 27 | 28 | ?> 29 | 30 | -------------------------------------------------------------------------------- /tools/gene_enrichment_ajax.php: -------------------------------------------------------------------------------- 1 | 2 | 47 | -------------------------------------------------------------------------------- /tools/get_annotation_types.php: -------------------------------------------------------------------------------- 1 | 17 | -------------------------------------------------------------------------------- /tools/passport/01_list_pass_files.php: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
    5 |

    Passport

    6 |
    7 | 55 |
    56 |
    57 | 58 | 59 | 60 | 61 | -------------------------------------------------------------------------------- /tools/passport/passport_ajax.php: -------------------------------------------------------------------------------- 1 | >"); 29 | array_push($html_array, ""); 30 | array_push($html_array, ""); 31 | array_push($html_array, ""); 32 | array_push($html_array, ""); 33 | 34 | } else { 35 | foreach (array_filter($shell_array) as $option) { 36 | array_push($html_array,""); 37 | } 38 | } 39 | 40 | // echo json_encode($shell_res); 41 | $shell_res = ""; 42 | echo json_encode($html_array); 43 | 44 | 45 | ?> 46 | -------------------------------------------------------------------------------- /tools/passport/passport_table_ajax.php: -------------------------------------------------------------------------------- 1 | "); 21 | // array_push($html_array,"
    "); 22 | array_push($html_array,"\n"); 23 | 24 | $field_number = 0; 25 | 26 | // // TABLE HEADER 27 | array_push($html_array,"\n"); 28 | 29 | foreach ($header_cols as $head_index => $hcol) { 30 | 31 | array_push($html_array,""); 32 | 33 | // find column index for unique identifier that will link to accession info 34 | if ($unique_link == $hcol) { 35 | $field_number = $head_index; 36 | } 37 | } //close foreach 38 | 39 | array_push($html_array, ""); 40 | 41 | foreach ($tab_file as $line) { 42 | $columns = explode("\t", $line); 43 | array_push($html_array, ""); 44 | foreach ($columns as $col_index => $col) { 45 | if ($col_index == $field_number) { 46 | array_push($html_array,""); 47 | } else { 48 | array_push($html_array,""); 49 | } 50 | } // end foreach columns 51 | array_push($html_array,""); 52 | } // end foreach lines 53 | 54 | array_push($html_array,"
    $hcol
    $col$col


    "); 55 | 56 | echo json_encode($html_array); 57 | ?> 58 | 59 | 60 | -------------------------------------------------------------------------------- /tools/search/search_info_modal.php: -------------------------------------------------------------------------------- 1 | 2 | 35 | -------------------------------------------------------------------------------- /tools/vcf/ajax_get_gene_coordinates.php: -------------------------------------------------------------------------------- 1 | $col[0]$col[2]$col[3]$col[4]$col[6]$col[8]"); 18 | } 19 | //echo $gff_array; 20 | echo json_encode($gff_array) 21 | ?> 22 | --------------------------------------------------------------------------------