def iter_compath_dfs() -> Iterable[pd.DataFrame]:
"""Iterate over all ComPath mappings."""
sha = get_commit('ComPath', 'compath-resources')
yield _get_df('kegg_reactome.csv', sha=sha)
yield _get_df('kegg_wikipathways.csv', sha=sha)
yield _get_df('pathbank_kegg.csv', sha=sha)
yield _get_df('pathbank_reactome.csv', sha=sha)
yield _get_df('pathbank_wikipathways.csv', sha=sha)
yield _get_df('special_mappings.csv', sha=sha)
yield _get_df('wikipathways_reactome.csv', sha=sha)
def iter_compath_dfs() -> Iterable[pd.DataFrame]:
"""Iterate over all ComPath mappings."""
sha = get_commit("ComPath", "compath-resources")
yield _get_df("kegg_reactome.csv", sha=sha)
yield _get_df("kegg_wikipathways.csv", sha=sha)
yield _get_df("pathbank_kegg.csv", sha=sha)
yield _get_df("pathbank_reactome.csv", sha=sha)
yield _get_df("pathbank_wikipathways.csv", sha=sha)
yield _get_df("special_mappings.csv", sha=sha)
yield _get_df("wikipathways_reactome.csv", sha=sha)
def get_obo(force: bool = False) -> Obo:
"""Get FamPlex as OBO."""
version = get_commit('sorgerlab', 'famplex')
return Obo(
ontology=PREFIX,
name='FamPlex',
iter_terms=get_terms,
iter_terms_kwargs=dict(version=version, force=force),
data_version=version,
typedefs=[has_member, has_part, is_a, part_of],
auto_generated_by=f'bio2obo:{PREFIX}',
)
def get_biomappings_df() -> pd.DataFrame:
"""Get biomappings equivalences."""
sha = get_commit('biomappings', 'biomappings')
url = f'https://raw.githubusercontent.com/biomappings/biomappings/{sha}/src/biomappings/resources/mappings.tsv'
df = pd.read_csv(url, sep='\t')
df[PROVENANCE] = url
df.rename(columns={
'source prefix': SOURCE_PREFIX,
'source identifier': SOURCE_ID,
'target prefix': TARGET_PREFIX,
'target identifier': TARGET_ID,
},
inplace=True)
df = df[XREF_COLUMNS]
return df
def get_biomappings_df() -> pd.DataFrame:
"""Get biomappings equivalences."""
sha = get_commit("biopragmatics", "biomappings")
url = f"https://raw.githubusercontent.com/biopragmatics/biomappings/{sha}/src/biomappings/resources/mappings.tsv"
df = pd.read_csv(url, sep="\t")
df[PROVENANCE] = url
df.rename(
columns={
"source prefix": SOURCE_PREFIX,
"source identifier": SOURCE_ID,
"target prefix": TARGET_PREFIX,
"target identifier": TARGET_ID,
},
inplace=True,
)
df = df[XREF_COLUMNS]
return df
def _get_version(self) -> str:
return get_commit("sorgerlab", "famplex")