├── .circleci └── config.yml ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ └── main.yml ├── .gitignore ├── .readthedocs.yml ├── CITATION.cff ├── LICENSE ├── Makefile ├── README.md ├── _config.yml ├── assets ├── bioconda-badge-wide.png ├── cazy_web_logo.svg └── cazy_webscraper_v2.3+.svg ├── cazy_webscraper ├── __init__.py ├── api │ ├── __init__.py │ └── cw_query_database.py ├── cache │ ├── __init__.py │ ├── cazy.py │ ├── ncbi.py │ └── uniprot.py ├── cazy │ └── __init__.py ├── cazy_scraper.py ├── crawler │ ├── __init__.py │ └── get_validation_data.py ├── expand │ ├── __init__.py │ ├── extract_seqs │ │ ├── __init__.py │ │ └── extract_db_seqs.py │ ├── genbank │ │ ├── __init__.py │ │ ├── genomes │ │ │ ├── __init__.py │ │ │ ├── entrez.py │ │ │ └── get_genome_accs.py │ │ ├── sequences │ │ │ ├── __init__.py │ │ │ └── get_genbank_sequences.py │ │ └── taxonomy │ │ │ ├── __init__.py │ │ │ └── get_ncbi_taxs.py │ ├── gtdb │ │ ├── __init__.py │ │ └── get_gtdb_tax.py │ ├── pdb │ │ ├── __init__.py │ │ └── get_pdb_structures.py │ └── uniprot │ │ ├── __init__.py │ │ └── get_uniprot_data.py ├── ncbi │ ├── __init__.py │ ├── gene_names │ │ └── __init__.py │ ├── genomes │ │ └── __init__.py │ ├── sequences │ │ └── __init__.py │ └── taxonomy │ │ ├── __init__.py │ │ ├── lineage.py │ │ └── multiple_taxa.py ├── sql │ ├── __init__.py │ ├── get_schema.py │ ├── sql_interface │ │ ├── __init__.py │ │ ├── add_data │ │ │ ├── __init__.py │ │ │ ├── add_cazyme_data.py │ │ │ ├── add_genbank_data.py │ │ │ ├── add_genome_data.py │ │ │ ├── add_gtdb_tax.py │ │ │ ├── add_ncbi_tax_data.py │ │ │ └── add_uniprot_data.py │ │ ├── delete_data │ │ │ └── __init__.py │ │ └── get_data │ │ │ ├── __init__.py │ │ │ ├── get_api_data.py │ │ │ ├── get_assemblies.py │ │ │ ├── get_records.py │ │ │ ├── get_selected_gbks.py │ │ │ ├── get_selected_pdbs.py │ │ │ ├── get_table_dicts.py │ │ │ └── get_taxonomies.py │ └── sql_orm.py └── utilities │ ├── __init__.py │ ├── parse_configuration │ ├── __init__.py │ ├── cazy_class_synonym_dict.py │ └── cazy_dictionary.json │ └── parsers │ ├── __init__.py │ ├── api_parser.py │ ├── cazy_webscraper_parser.py │ ├── extract_seq_parser.py │ ├── gbk_seq_parser.py │ ├── get_genomes_parser.py │ ├── get_gtdb_parser.py │ ├── get_schema_parser.py │ ├── pdb_strctre_parser.py │ ├── tax_ncbi_parser.py │ └── uniprot_parser.py ├── codecov.yml ├── configuration_files ├── README.md ├── example_cazy_config.yaml ├── example_get_data_config.yaml ├── template_cazy_config.yaml └── template_get_data_config.yaml ├── coverage.xml ├── database_schema.pdf ├── docs ├── Makefile ├── api.rst ├── apitutorial.rst ├── cache.rst ├── cazy_web_logo.svg ├── cazy_webscraper_version2.svg ├── citation.rst ├── conf.py ├── contributing.rst ├── database.rst ├── genbank.rst ├── genbanktutorial.rst ├── genomes.rst ├── genomestutorial.rst ├── gtdbtax.rst ├── gtdbtaxtutorial.rst ├── index.rst ├── installation.rst ├── integrate.rst ├── license.rst ├── ncbitax.rst ├── ncbitaxtutorial.rst ├── pdb.rst ├── pdbtutorial.rst ├── quickstart.rst ├── schema.rst ├── sequence.rst ├── sequencetutorial.rst ├── tutorial.rst ├── uniprot.rst ├── uniprottutorial.rst └── usage.rst ├── environment.yml ├── getting_started_cazy_webscraper_v2.pdf ├── manuscript ├── MS_supplementary_material.zip └── README.md ├── requirements-dev.txt ├── requirements-pip.txt ├── requirements.txt ├── setup.py └── tests ├── conftest.py ├── test_add_cazymes.py ├── test_api.py ├── test_cazy_init.py ├── test_crawler.py ├── test_cw_init.py ├── test_expand.py ├── test_extract_seqs.py ├── test_get_ncbi_tax.py ├── test_gtdb.py ├── test_inputs ├── cazy_dictionary.json ├── test_inputs_cazy │ ├── cazy_data.txt │ └── cazy_db_time_stamp.zip ├── test_inputs_crawler │ ├── cazy_classpage_no_subfams.html │ ├── class_url_pages │ │ ├── README.md │ │ ├── cazy_homepage.html │ │ ├── cazy_homepage_no_spip_out.html │ │ └── cazy_homepage_no_urls.html │ ├── family_url_pages │ │ ├── DEL_cazy_classpage_incorrect_urls.html │ │ ├── README.md │ │ ├── cazy_classpage.html │ │ └── cazy_classpage_no_urls.html │ ├── subfamily_urls.txt │ └── test_family_urls.txt ├── test_inputs_gtdb │ ├── ar53_taxonomy.tsv.gz │ └── gtdb_page.html ├── test_inputs_ncbi_genomes │ ├── efetch_accession_results.xml │ ├── elink_prot_nuccore.xml │ └── esummary.xml ├── test_inputs_ncbi_tax │ ├── efetchLinkedProteins.xml │ ├── efetchTaxLineage.xml │ ├── elinkProtTax.xml │ ├── entrezProt.xml │ ├── epost.xml │ ├── prot_ids.out │ ├── test_accs.txt │ └── test_lineage_cache.json ├── test_inputs_parse │ └── sequence.fasta ├── test_inputs_parse_configuration │ └── config_file.yaml ├── test_inputs_sql_interface │ └── test_accs.txt ├── test_inputs_webscraper │ ├── family_urls.txt │ └── proteins.txt └── unit_test_database │ ├── README.md │ ├── blank_db.db │ └── unit_test_23-05-22.db ├── test_ncbi.py ├── test_ncbi_genomes.py ├── test_orm.py ├── test_outputs ├── test_api │ ├── test__db_path_gbkAcc.csv │ └── 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