├── .bumpversion.cfg ├── .codecov.yml ├── .flake8 ├── .gitignore ├── .readthedocs.yml ├── .travis.yml ├── AUTHORS.rst ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile └── source │ ├── cli.rst │ ├── conf.py │ ├── constants.rst │ ├── index.rst │ ├── kegg.rst │ ├── reactome.rst │ ├── utils.rst │ └── wikipathways.rst ├── setup.cfg ├── setup.py ├── src └── pathme │ ├── __init__.py │ ├── __main__.py │ ├── cli.py │ ├── constants.py │ ├── export_utils.py │ ├── kegg │ ├── __init__.py │ ├── __main__.py │ ├── cli.py │ ├── convert_to_bel.py │ ├── kegg_xml_parser.py │ └── utils.py │ ├── mappings_parser.py │ ├── normalize_names.py │ ├── pybel_utils.py │ ├── reactome │ ├── __init__.py │ ├── __main__.py │ ├── cli.py │ ├── convert_to_bel.py │ ├── rdf_sparql.py │ └── utils.py │ ├── utils.py │ └── wikipathways │ ├── __init__.py │ ├── __main__.py │ ├── cli.py │ ├── convert_to_bel.py │ ├── json_rdf_parser.py │ ├── rdf_sparql.py │ └── utils.py ├── tests ├── __init__.py ├── constants.py ├── resources │ ├── chebi_test.tsv.gz │ ├── hgnc_test.json │ ├── kegg │ │ ├── 03320_cpd_test.xml │ │ ├── hsa00010.xml │ │ ├── hsa04150_pmod_test.xml │ │ └── hsa04330.xml │ └── wp │ │ ├── WP107.ttl │ │ ├── WP111.ttl │ │ ├── WP1871.ttl │ │ ├── WP22.ttl │ │ ├── WP2359_mod.ttl │ │ ├── WP2799.ttl │ │ └── WP706.ttl ├── test_kegg │ ├── __init__.py │ └── test_kegg.py ├── test_shared │ ├── __init__.py │ └── test_utils.py └── test_wikipathways │ ├── __init__.py │ ├── test_custom_parser_wikipathways.py │ └── test_wikipathways.py └── tox.ini /.bumpversion.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PathwayMerger/PathMe/HEAD/.bumpversion.cfg -------------------------------------------------------------------------------- /.codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PathwayMerger/PathMe/HEAD/.codecov.yml 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