├── .gitattributes ├── .github └── workflows │ └── chewbbaca.yml ├── .gitignore ├── .readthedocs.yaml ├── CHANGELOG.md ├── CHEWBBACA ├── AlleleCall │ ├── __init__.py │ └── allele_call.py ├── AlleleCallEvaluator │ ├── __init__.py │ └── evaluate_calls.py ├── CHEWBBACA_NS │ ├── __init__.py │ ├── download_schema.py │ ├── stats_requests.py │ ├── synchronize_schema.py │ └── upload_schema.py ├── ComputeMSA │ └── compute_msa.py ├── CreateSchema │ ├── __init__.py │ └── create_schema.py ├── ExtractCgMLST │ ├── __init__.py │ └── determine_cgmlst.py ├── GetAlleles │ └── get_alleles.py ├── PrepExternalSchema │ ├── __init__.py │ └── adapt_schema.py ├── SchemaEvaluator │ ├── __init__.py │ └── evaluate_schema.py ├── UniprotFinder │ ├── __init__.py │ └── annotate_schema.py ├── __init__.py ├── chewBBACA.py ├── prodigal_training_files │ ├── Acinetobacter_baumannii.trn │ ├── Campylobacter_jejuni.trn │ ├── Enterococcus_faecium.trn │ ├── Escherichia_coli.trn │ ├── Haemophilus_influenzae.trn │ ├── Klebsiella_pneumoniae.trn │ ├── Legionella_pneumophila.trn │ ├── Listeria_monocytogenes.trn │ ├── Pseudomonas_aeruginosa.trn │ ├── README.md │ ├── Salmonella_enterica.trn │ ├── Staphylococcus_aureus.trn │ ├── Staphylococcus_haemolyticus.trn │ ├── Streptococcus_agalactiae.trn │ ├── Streptococcus_canis.trn │ ├── Streptococcus_dysgalactiae.trn │ ├── Streptococcus_equi.trn │ ├── Streptococcus_pneumoniae.trn │ ├── Streptococcus_pyogenes.trn │ └── Yersinia_enterocolitica.trn ├── report_template_components │ ├── babel.config.js │ ├── package-lock.json │ ├── package.json │ ├── src │ │ ├── bundles │ │ │ ├── AlleleCallEvaluator │ │ │ │ └── report_bundle.js │ │ │ └── SchemaEvaluator │ │ │ │ ├── loci_reports │ │ │ │ └── report_bundle.js │ │ │ │ └── schema_report │ │ │ │ └── report_bundle.js │ │ ├── components │ │ │ ├── AccordionMUI.js │ │ │ ├── AlertMUI.js │ │ │ ├── App.js │ │ │ ├── DataTable.js │ │ │ ├── MSA.js │ │ │ ├── PhylogeneticTree.js │ │ │ ├── PlotlyPlot.js │ │ │ └── TabPanelMUI.js │ │ ├── constants.js │ │ ├── index.js │ │ └── pages │ │ │ ├── AlleleCallEvaluator │ │ │ ├── ReportPage.css │ │ │ └── ReportPage.js │ │ │ └── SchemaEvaluator │ │ │ ├── loci_reports │ │ │ ├── ReportPage.css │ │ │ └── ReportPage.js │ │ │ └── schema_report │ │ │ ├── ReportPage.css │ │ │ └── ReportPage.js │ └── webpack.config.js ├── requirements.txt └── utils │ ├── __init__.py │ ├── blast_wrapper.py │ ├── chewiens_requests.py │ ├── constants.py │ ├── core_functions.py │ ├── distance_matrix.py │ ├── fasta_operations.py │ ├── fasttree_wrapper.py │ ├── file_operations.py │ ├── gene_prediction.py │ ├── iterables_manipulation.py │ ├── join_profiles.py │ ├── mafft_wrapper.py │ ├── multiprocessing_operations.py │ ├── parameters_validation.py │ ├── process_datetime.py │ ├── profile_hasher.py │ ├── profiles_sqlitedb.py │ ├── remove_genes.py │ ├── sequence_clustering.py │ ├── sequence_manipulation.py │ └── uniprot_requests.py ├── CITATION.cff ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── pyproject.toml └── setup.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/chewbbaca.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/.github/workflows/chewbbaca.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CHEWBBACA/AlleleCall/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/AlleleCall/allele_call.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/AlleleCall/allele_call.py -------------------------------------------------------------------------------- /CHEWBBACA/AlleleCallEvaluator/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/AlleleCallEvaluator/evaluate_calls.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/AlleleCallEvaluator/evaluate_calls.py -------------------------------------------------------------------------------- /CHEWBBACA/CHEWBBACA_NS/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/CHEWBBACA_NS/download_schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/CHEWBBACA_NS/download_schema.py -------------------------------------------------------------------------------- /CHEWBBACA/CHEWBBACA_NS/stats_requests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/CHEWBBACA_NS/stats_requests.py -------------------------------------------------------------------------------- /CHEWBBACA/CHEWBBACA_NS/synchronize_schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/CHEWBBACA_NS/synchronize_schema.py -------------------------------------------------------------------------------- /CHEWBBACA/CHEWBBACA_NS/upload_schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/CHEWBBACA_NS/upload_schema.py -------------------------------------------------------------------------------- /CHEWBBACA/ComputeMSA/compute_msa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/ComputeMSA/compute_msa.py -------------------------------------------------------------------------------- /CHEWBBACA/CreateSchema/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/CreateSchema/create_schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/CreateSchema/create_schema.py -------------------------------------------------------------------------------- /CHEWBBACA/ExtractCgMLST/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/ExtractCgMLST/determine_cgmlst.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/ExtractCgMLST/determine_cgmlst.py -------------------------------------------------------------------------------- /CHEWBBACA/GetAlleles/get_alleles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/GetAlleles/get_alleles.py -------------------------------------------------------------------------------- /CHEWBBACA/PrepExternalSchema/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/PrepExternalSchema/adapt_schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/PrepExternalSchema/adapt_schema.py -------------------------------------------------------------------------------- /CHEWBBACA/SchemaEvaluator/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/SchemaEvaluator/evaluate_schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/SchemaEvaluator/evaluate_schema.py -------------------------------------------------------------------------------- /CHEWBBACA/UniprotFinder/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/UniprotFinder/annotate_schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/UniprotFinder/annotate_schema.py -------------------------------------------------------------------------------- /CHEWBBACA/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | __version__ = "3.5.0" 3 | -------------------------------------------------------------------------------- /CHEWBBACA/chewBBACA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/chewBBACA.py -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Acinetobacter_baumannii.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Acinetobacter_baumannii.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Campylobacter_jejuni.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Campylobacter_jejuni.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Enterococcus_faecium.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Enterococcus_faecium.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Escherichia_coli.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Escherichia_coli.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Haemophilus_influenzae.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Haemophilus_influenzae.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Klebsiella_pneumoniae.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Klebsiella_pneumoniae.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Legionella_pneumophila.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Legionella_pneumophila.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Listeria_monocytogenes.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Listeria_monocytogenes.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Pseudomonas_aeruginosa.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Pseudomonas_aeruginosa.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/README.md -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Salmonella_enterica.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Salmonella_enterica.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Staphylococcus_aureus.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Staphylococcus_aureus.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Staphylococcus_haemolyticus.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Staphylococcus_haemolyticus.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Streptococcus_agalactiae.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Streptococcus_agalactiae.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Streptococcus_canis.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Streptococcus_canis.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Streptococcus_dysgalactiae.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Streptococcus_dysgalactiae.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Streptococcus_equi.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Streptococcus_equi.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Streptococcus_pneumoniae.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Streptococcus_pneumoniae.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Streptococcus_pyogenes.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Streptococcus_pyogenes.trn -------------------------------------------------------------------------------- /CHEWBBACA/prodigal_training_files/Yersinia_enterocolitica.trn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/prodigal_training_files/Yersinia_enterocolitica.trn -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/babel.config.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/babel.config.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/package-lock.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/package-lock.json -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/package.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/package.json -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/bundles/AlleleCallEvaluator/report_bundle.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/bundles/AlleleCallEvaluator/report_bundle.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/bundles/SchemaEvaluator/loci_reports/report_bundle.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/bundles/SchemaEvaluator/loci_reports/report_bundle.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/bundles/SchemaEvaluator/schema_report/report_bundle.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/bundles/SchemaEvaluator/schema_report/report_bundle.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/components/AccordionMUI.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/components/AccordionMUI.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/components/AlertMUI.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/components/AlertMUI.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/components/App.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/components/App.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/components/DataTable.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/components/DataTable.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/components/MSA.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/components/MSA.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/components/PhylogeneticTree.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/components/PhylogeneticTree.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/components/PlotlyPlot.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/components/PlotlyPlot.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/components/TabPanelMUI.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/components/TabPanelMUI.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/constants.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/constants.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/index.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/index.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/pages/AlleleCallEvaluator/ReportPage.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/pages/AlleleCallEvaluator/ReportPage.css -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/pages/AlleleCallEvaluator/ReportPage.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/pages/AlleleCallEvaluator/ReportPage.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/pages/SchemaEvaluator/loci_reports/ReportPage.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/pages/SchemaEvaluator/loci_reports/ReportPage.css -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/pages/SchemaEvaluator/loci_reports/ReportPage.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/pages/SchemaEvaluator/loci_reports/ReportPage.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/pages/SchemaEvaluator/schema_report/ReportPage.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/pages/SchemaEvaluator/schema_report/ReportPage.css -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/src/pages/SchemaEvaluator/schema_report/ReportPage.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/src/pages/SchemaEvaluator/schema_report/ReportPage.js -------------------------------------------------------------------------------- /CHEWBBACA/report_template_components/webpack.config.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/report_template_components/webpack.config.js -------------------------------------------------------------------------------- /CHEWBBACA/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/requirements.txt -------------------------------------------------------------------------------- /CHEWBBACA/utils/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /CHEWBBACA/utils/blast_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/blast_wrapper.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/chewiens_requests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/chewiens_requests.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/constants.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/core_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/core_functions.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/distance_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/distance_matrix.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/fasta_operations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/fasta_operations.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/fasttree_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/fasttree_wrapper.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/file_operations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/file_operations.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/gene_prediction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/gene_prediction.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/iterables_manipulation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/iterables_manipulation.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/join_profiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/join_profiles.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/mafft_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/mafft_wrapper.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/multiprocessing_operations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/multiprocessing_operations.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/parameters_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/parameters_validation.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/process_datetime.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/process_datetime.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/profile_hasher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/profile_hasher.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/profiles_sqlitedb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/profiles_sqlitedb.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/remove_genes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/remove_genes.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/sequence_clustering.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/sequence_clustering.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/sequence_manipulation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/sequence_manipulation.py -------------------------------------------------------------------------------- /CHEWBBACA/utils/uniprot_requests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CHEWBBACA/utils/uniprot_requests.py -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/CITATION.cff -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/README.md -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/pyproject.toml -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/B-UMMI/chewBBACA/HEAD/setup.py --------------------------------------------------------------------------------