pysec2pri 0.0.2__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pysec2pri/__init__.py +78 -0
- pysec2pri/__main__.py +12 -0
- pysec2pri/api.py +871 -0
- pysec2pri/cli.py +719 -0
- pysec2pri/config/__init__.py +1 -0
- pysec2pri/config/chebi.yaml +144 -0
- pysec2pri/config/hgnc.yaml +127 -0
- pysec2pri/config/hmdb.yaml +128 -0
- pysec2pri/config/ncbi.yaml +131 -0
- pysec2pri/config/uniprot.yaml +127 -0
- pysec2pri/config/wikidata.yaml +127 -0
- pysec2pri/constants.py +31 -0
- pysec2pri/diff.py +345 -0
- pysec2pri/download.py +782 -0
- pysec2pri/exports.py +401 -0
- pysec2pri/logging.py +65 -0
- pysec2pri/parsers/__init__.py +38 -0
- pysec2pri/parsers/base.py +1304 -0
- pysec2pri/parsers/chebi.py +655 -0
- pysec2pri/parsers/hgnc.py +383 -0
- pysec2pri/parsers/hmdb.py +293 -0
- pysec2pri/parsers/ncbi.py +274 -0
- pysec2pri/parsers/uniprot.py +210 -0
- pysec2pri/parsers/wikidata.py +524 -0
- pysec2pri/py.typed +1 -0
- pysec2pri/queries/__init__.py +118 -0
- pysec2pri/queries/chemical_redirects.rq +33 -0
- pysec2pri/queries/chemical_redirects_test.rq +34 -0
- pysec2pri/queries/gene_redirects.rq +22 -0
- pysec2pri/queries/gene_redirects_test.rq +23 -0
- pysec2pri/queries/protein_redirects.rq +30 -0
- pysec2pri/queries/protein_redirects_test.rq +31 -0
- pysec2pri/update_ids.py +404 -0
- pysec2pri/version.py +39 -0
- pysec2pri-0.0.2.dist-info/METADATA +181 -0
- pysec2pri-0.0.2.dist-info/RECORD +39 -0
- pysec2pri-0.0.2.dist-info/WHEEL +4 -0
- pysec2pri-0.0.2.dist-info/entry_points.txt +3 -0
- pysec2pri-0.0.2.dist-info/licenses/LICENSE +21 -0
pysec2pri/__init__.py
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"""Secondary to primary identifier mapping.
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This package provides tools for converting secondary (retired/withdrawn)
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identifiers to primary (current) identifiers across various biological
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databases including ChEBI, HMDB, HGNC, NCBI Gene, and UniProt.
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"""
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from pysec2pri.api import (
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generate_chebi,
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generate_chebi_synonyms,
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generate_hgnc,
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generate_hgnc_primary_ids,
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generate_hgnc_symbols,
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generate_hmdb,
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generate_hmdb_proteins,
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generate_ncbi,
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generate_ncbi_symbols,
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generate_uniprot,
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generate_wikidata,
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generate_wikidata_symbols,
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resolve_ids,
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resolve_symbols,
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write_json,
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write_name2synonym,
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write_output,
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write_owl,
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write_rdf,
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write_sec2pri,
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write_sssom,
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write_symbol_sec2pri,
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)
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from pysec2pri.parsers.base import (
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WITHDRAWN_ENTRY,
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WITHDRAWN_ENTRY_LABEL,
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IdMappingSet,
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LabelMappingSet,
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Sec2PriMappingSet,
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)
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from pysec2pri.update_ids import build_lookup, build_symbol_lookup, update_ids, update_symbols
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__all__ = [
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# Sentinel values
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"WITHDRAWN_ENTRY",
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"WITHDRAWN_ENTRY_LABEL",
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# Mapping Set classes
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"IdMappingSet",
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"LabelMappingSet",
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"Sec2PriMappingSet",
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# ID resolution
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"build_lookup",
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"build_symbol_lookup",
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# generate_* (download + parse in one call)
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"generate_chebi",
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"generate_chebi_synonyms",
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"generate_hgnc",
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"generate_hgnc_primary_ids",
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"generate_hgnc_symbols",
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"generate_hmdb",
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"generate_hmdb_proteins",
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"generate_ncbi",
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"generate_ncbi_symbols",
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"generate_uniprot",
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"generate_wikidata",
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"generate_wikidata_symbols",
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"resolve_ids",
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"resolve_symbols",
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"update_ids",
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"update_symbols",
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# Export functions
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"write_json",
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"write_name2synonym",
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"write_output",
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"write_owl",
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"write_rdf",
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"write_sec2pri",
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"write_sssom",
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"write_symbol_sec2pri",
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]
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pysec2pri/__main__.py
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"""Entrypoint module, in case you use `python -m pysec2pri`.
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Why does this file exist, and why ``__main__``? For more info, read:
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- https://www.python.org/dev/peps/pep-0338/
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- https://docs.python.org/3/using/cmdline.html#cmdoption-m
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"""
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from .cli import main
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if __name__ == "__main__":
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main()
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