def _ensure_conv_genome_helper(
kegg_genome_id: str,
target_database: str,
*,
version: str,
error_on_missing: bool = False,
) -> Optional[str]:
"""Get the KEGG-external protein map for the given organism/database."""
name = f"{kegg_genome_id}.tsv"
try:
rv = ensure_path(
KEGG_GENES_PREFIX,
f"conv_{target_database}",
url=f"{BASE}/conv/{target_database}/{kegg_genome_id}",
name=name,
error_on_missing=error_on_missing,
version=version,
)
except urllib.error.HTTPError:
path_rv = prefix_directory_join(
KEGG_GENES_PREFIX,
f"conv_{target_database}",
name=name,
version=version,
)
with path_rv.open("w") as file:
print(file=file) # noqa: T201
return path_rv.as_posix()
except FileNotFoundError:
return None
else:
return rv
def ensure_list_genomes(version: str) -> str:
"""Ensure the KEGG Genome file is downloaded."""
return ensure_path(
KEGG_GENOME_PREFIX,
url=f"{BASE}/list/genome",
name="genome.tsv",
version=version,
)
def ensure_list_genome(kegg_genome_id: str, *, version: str) -> str:
"""Get the list of genes for the given organism."""
return ensure_path(
KEGG_GENES_PREFIX,
"genes",
url=f"{BASE}/list/{kegg_genome_id}",
name=f"{kegg_genome_id}.tsv",
version=version,
)
def ensure_list_pathway_genome(kegg_genome_id: str,
*,
version: str,
error_on_missing: bool = False) -> str:
"""Get the list of pathways for the given organism.
:raises: FileNotFoundError
"""
return ensure_path(
KEGG_PATHWAY_PREFIX,
"pathways",
url=f"{BASE}/list/pathway/{kegg_genome_id}",
name=f"{kegg_genome_id}.tsv",
error_on_missing=error_on_missing,
version=version,
)
def ensure_link_pathway_genome(kegg_genome_id: str,
*,
version: str,
error_on_missing: bool = False) -> str:
"""Get the protein-pathway links for the given organism.
:raises: FileNotFoundError
"""
return ensure_path(
KEGG_PATHWAY_PREFIX,
'link_pathway',
url=f'{BASE}/link/pathway/{kegg_genome_id}',
name=f'{kegg_genome_id}.tsv',
error_on_missing=error_on_missing,
version=version,
)