bin/prophane
opt/prophane/LICENSE
opt/prophane/README.md
opt/prophane/Snakefile
opt/prophane/Snakefile_db_setup.smk
opt/prophane/build_env_setup.sh
opt/prophane/changelog.md
opt/prophane/conda_build.sh
opt/prophane/documentation/ProphaneOverview.pptx
opt/prophane/environment.yaml
opt/prophane/envs/diamond.yaml
opt/prophane/envs/emapper_v1.yaml
opt/prophane/envs/emapper_v2.yaml
opt/prophane/envs/hmmer-3-0.yaml
opt/prophane/envs/hmmer-latest.yaml
opt/prophane/envs/hmmer.yaml.old
opt/prophane/envs/krona.yaml
opt/prophane/envs/mafft.yaml
opt/prophane/metadata_conda_debug.yaml
opt/prophane/prophane.py
opt/prophane/prophane_workflow.md
opt/prophane/rules/analysis/create_info.smk
opt/prophane/rules/analysis/create_krona.smk
opt/prophane/rules/analysis/create_pg_fasta.smk
opt/prophane/rules/analysis/create_summary.smk
opt/prophane/rules/analysis/lca_task.smk
opt/prophane/rules/analysis/map_to_seq.smk
opt/prophane/rules/analysis/parse_search_result_into_protein_groups_sql_db.smk
opt/prophane/rules/analysis/quant_pg.smk
opt/prophane/rules/analysis/quant_task.smk
opt/prophane/rules/analysis/report_mafft.smk
opt/prophane/rules/analysis/run_acc2annot_mapper.smk
opt/prophane/rules/analysis/run_diamond.smk
opt/prophane/rules/analysis/run_emapper.smk
opt/prophane/rules/analysis/run_hmmer.smk
opt/prophane/rules/analysis/run_mafft.smk
opt/prophane/rules/analysis/tax_by_taxmap.smk
opt/prophane/rules/db_setup/check_md5.smk
opt/prophane/rules/db_setup/create_db_cfg_yaml.smk
opt/prophane/rules/db_setup/create_skip_files.smk
opt/prophane/rules/db_setup/download_database_file.smk
opt/prophane/rules/db_setup/gunzip.smk
opt/prophane/rules/db_setup/make_dbcan_map.smk
opt/prophane/rules/db_setup/make_dmnd_db.smk
opt/prophane/rules/db_setup/make_eggnog_map.smk
opt/prophane/rules/db_setup/make_foam_map.smk
opt/prophane/rules/db_setup/make_hmm_lib.smk
opt/prophane/rules/db_setup/make_nr_acc2tax_map.smk
opt/prophane/rules/db_setup/make_nr_tax2annot_map.smk
opt/prophane/rules/db_setup/make_pfam_map.smk
opt/prophane/rules/db_setup/make_resfam_map.smk
opt/prophane/rules/db_setup/make_tigrfam_map.smk
opt/prophane/rules/db_setup/make_uniprot_acc2tax_map.smk
opt/prophane/rules/db_setup/make_uniprot_tax2annot_map.smk
opt/prophane/schemas/config.schema.yaml
opt/prophane/schemas/general_config.schema.yaml
opt/prophane/scripts/batch_config_creator.py
opt/prophane/scripts/create_job_taxmap.ipynb
opt/prophane/scripts/format4krona.py
opt/prophane/scripts/parse_proteome_discoverer_output.py
opt/prophane/sources/images/.gitkeep
opt/prophane/sources/images/prophane_workflow.png
opt/prophane/styles/generic.yaml
opt/prophane/styles/mpa_1_8_x.yaml
opt/prophane/styles/mpa_server_multisample.yaml
opt/prophane/styles/mzident_1_2_0.yaml
opt/prophane/styles/mztab_1_0_0.yaml
opt/prophane/styles/proteome_discoverer_2_5.yaml
opt/prophane/styles/scaffold_4_8_x.yaml
opt/prophane/templates/README_databases.md
opt/prophane/templates/config/README.md
opt/prophane/templates/config/config.yaml
opt/prophane/templates/input/accession2annotation_map.tsv
opt/prophane/templates/input/generic_table.txt
opt/prophane/test.sh
opt/prophane/test_environment.yaml
opt/prophane/tests/README.md
opt/prophane/tests/__init__.py
opt/prophane/tests/conftest.py
opt/prophane/tests/creation_scripts_for_test_data/create_nr_taxdump_test_db.py
opt/prophane/tests/creation_scripts_for_test_data/extract_from_hmmlib.py
opt/prophane/tests/creation_scripts_for_test_data/update_sql_db_print_db_methods.py
opt/prophane/tests/example_test_job/input/config.yaml
opt/prophane/tests/example_test_job/input/protein_report.xls
opt/prophane/tests/example_test_job/input/target_db.fasta
opt/prophane/tests/integration_tests/mztab_parser/expected_results/maxquant_pg_db.sql
opt/prophane/tests/integration_tests/mztab_parser/expected_results/pd_example_pg_db.sql
opt/prophane/tests/integration_tests/mztab_parser/job/pd_mztab_example.mztab
opt/prophane/tests/integration_tests/mztab_parser/test_mztab_parser.py
opt/prophane/tests/integration_tests/pd_parser/expected_results/protein_groups_error_test_db.sql
opt/prophane/tests/integration_tests/pd_parser/expected_results/result1_protein_groups_db.sql
opt/prophane/tests/integration_tests/pd_parser/expected_results/result2_protein_groups_db.sql
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opt/prophane/tests/integration_tests/pd_parser/job/error_test.xlsx
opt/prophane/tests/integration_tests/pd_parser/job/proteome_discoverer_test.xlsx
opt/prophane/tests/integration_tests/pd_parser/test_pd_parser.py
opt/prophane/tests/integration_tests/read_spectra_from_db/protein_groups_db.sql
opt/prophane/tests/integration_tests/read_spectra_from_db/test_get_spectra_per_acc_from_pg_db.py
opt/prophane/tests/integration_tests/test_config.py
opt/prophane/tests/integration_tests/weighted_lca/__init__.py
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opt/prophane/tests/integration_tests/weighted_lca/resources/job_resources_with_spectra/protein_groups.yaml
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opt/prophane/tests/integration_tests/weighted_lca/resources/job_resources_with_spectra/with_spectra_protein_groups.yaml
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opt/prophane/tests/resources/test_cazy_db_result_mapping/job_dir/input/config.yaml
opt/prophane/tests/resources/test_cazy_db_result_mapping/job_dir/pgs/protein_groups_db.sql
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opt/prophane/tests/resources/test_db_preprocessing/expected-dbs/db_setup_config.yaml
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opt/prophane/tests/resources/test_db_preprocessing/expected-dbs/foam/rel1a/db_config.yaml
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opt/prophane/tests/resources/test_db_preprocessing/expected-dbs/ncbi_accession2taxid/2018-08-08/db_config.yaml
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opt/prophane/tests/unit_tests/db_handling/test_migrate_database_schema_version.py
opt/prophane/tests/unit_tests/progs/__init__.py
opt/prophane/tests/unit_tests/progs/test_acc2annot_mapper.py
opt/prophane/tests/unit_tests/test_fasta_handling.py
opt/prophane/tests/unit_tests/weighted_lca/__init__.py
opt/prophane/tests/unit_tests/weighted_lca/test_weight_lca.py
opt/prophane/utils/__init__.py
opt/prophane/utils/config.py
opt/prophane/utils/create_best_hits.py
opt/prophane/utils/create_summary.py
opt/prophane/utils/create_task_map.py
opt/prophane/utils/databases/__init__.py
opt/prophane/utils/databases/api_class.py
opt/prophane/utils/databases/dbcan/__init__.py
opt/prophane/utils/databases/dbcan/dbcan.py
opt/prophane/utils/databases/dbcan/dbcan.yaml.template
opt/prophane/utils/databases/dbcan/dbcan_res.yaml
opt/prophane/utils/databases/eggnog/__init__.py
opt/prophane/utils/databases/eggnog/eggnog.py
opt/prophane/utils/databases/eggnog/eggnog_v4.yaml.template
opt/prophane/utils/databases/eggnog/eggnog_v4_res.yaml
opt/prophane/utils/databases/eggnog/eggnog_v5.yaml.template
opt/prophane/utils/databases/eggnog/eggnog_v5_res.yaml
opt/prophane/utils/databases/foam/__init__.py
opt/prophane/utils/databases/foam/foam.py
opt/prophane/utils/databases/foam/foam.yaml.template
opt/prophane/utils/databases/foam/foam_res.yaml
opt/prophane/utils/databases/ncbi/__init__.py
opt/prophane/utils/databases/ncbi/ncbi_accession2taxid.py
opt/prophane/utils/databases/ncbi/ncbi_accession2taxid.yaml.template
opt/prophane/utils/databases/ncbi/ncbi_accession2taxid_res.yaml
opt/prophane/utils/databases/ncbi/ncbi_nr.py
opt/prophane/utils/databases/ncbi/ncbi_nr.yaml.template
opt/prophane/utils/databases/ncbi/ncbi_nr_res.yaml
opt/prophane/utils/databases/ncbi/ncbi_taxdump.py
opt/prophane/utils/databases/ncbi/ncbi_taxdump.yaml.template
opt/prophane/utils/databases/ncbi/ncbi_taxdump_res.yaml
opt/prophane/utils/databases/pfams/__init__.py
opt/prophane/utils/databases/pfams/pfams.py
opt/prophane/utils/databases/pfams/pfams.yaml.template
opt/prophane/utils/databases/pfams/pfams_res.yaml
opt/prophane/utils/databases/resfams/__init__.py
opt/prophane/utils/databases/resfams/resfams.py
opt/prophane/utils/databases/resfams/resfams_core.yaml.template
opt/prophane/utils/databases/resfams/resfams_core_res.yaml
opt/prophane/utils/databases/resfams/resfams_full.yaml.template
opt/prophane/utils/databases/resfams/resfams_full_res.yaml
opt/prophane/utils/databases/superclasses/__init__.py
opt/prophane/utils/databases/superclasses/database_superclasses.py
opt/prophane/utils/databases/superclasses/fasta_db_superclass.py
opt/prophane/utils/databases/superclasses/hmm_db_superclass.py
opt/prophane/utils/databases/tigrfams/__init__.py
opt/prophane/utils/databases/tigrfams/tigrfams.py
opt/prophane/utils/databases/tigrfams/tigrfams.yaml.template
opt/prophane/utils/databases/tigrfams/tigrfams_res.yaml
opt/prophane/utils/databases/uniprot/__init__.py
opt/prophane/utils/databases/uniprot/uniprot.py
opt/prophane/utils/databases/uniprot/uniprot_complete.yaml.template
opt/prophane/utils/databases/uniprot/uniprot_complete_res.yaml
opt/prophane/utils/databases/uniprot/uniprot_sp.yaml.template
opt/prophane/utils/databases/uniprot/uniprot_sp_res.yaml
opt/prophane/utils/databases/uniprot/uniprot_tax.yaml.template
opt/prophane/utils/databases/uniprot/uniprot_tax_res.yaml
opt/prophane/utils/databases/uniprot/uniprot_tr.yaml.template
opt/prophane/utils/databases/uniprot/uniprot_tr_res.yaml
opt/prophane/utils/db_handling/__init__.py
opt/prophane/utils/db_handling/db_access.py
opt/prophane/utils/db_handling/maintenance/__init__.py
opt/prophane/utils/db_handling/maintenance/migrate_database_schema_version.py
opt/prophane/utils/db_handling/maintenance/migrators.py
opt/prophane/utils/emapper_utils.py
opt/prophane/utils/exceptions.py
opt/prophane/utils/fasta_handling.py
opt/prophane/utils/helper_funcs.py
opt/prophane/utils/helper_funcs_for_snakemake_workflow.py
opt/prophane/utils/input_output.py
opt/prophane/utils/lca_determination/determine_lca.py
opt/prophane/utils/lca_determination/determine_summary_lca.py
opt/prophane/utils/lca_determination/lca_utils.py
opt/prophane/utils/lca_determination/weighted_lca_class.py
opt/prophane/utils/lca_determination/weighted_lca_on_full_summary.py
opt/prophane/utils/progs/__init__.py
opt/prophane/utils/progs/acc2annot_mapper.py
opt/prophane/utils/protein_group_sql_db.py
opt/prophane/utils/search_result_parsing/__init__.py
opt/prophane/utils/search_result_parsing/api_class.py
opt/prophane/utils/search_result_parsing/helper_classes.py
opt/prophane/utils/search_result_parsing/parse_generic_table.py
opt/prophane/utils/search_result_parsing/parse_mpa_metaprotein_report.py
opt/prophane/utils/search_result_parsing/parse_mpa_multisample_metaprotein_report.py
opt/prophane/utils/search_result_parsing/parse_mzident_report.py
opt/prophane/utils/search_result_parsing/parse_mztab.py
opt/prophane/utils/search_result_parsing/parse_proteome_discoverer.py
opt/prophane/utils/search_result_parsing/parse_scaffold_protein_report.py
opt/prophane/utils/search_result_parsing/style_handling.py
opt/prophane/utils/summary_classes.py
opt/prophane/utils/vars.py
