PFAM Annotation

annotate_pfam¶

Short description¶

Annotate PyMutation data with PFAM domains using database annotation or VEP data extraction.

Signature¶

def annotate_pfam(self, db_conn: Optional[duckdb.DuckDBPyConnection] = None, *, aa_column: str = 'aa_pos', auto_extract: bool = True, prefer_database: bool = True):

Parameters¶

Parameter	Type	Required	Description
`db_conn`	`Optional[duckdb.DuckDBPyConnection]`	No	DuckDB connection for PFAM database. If None, will create one automatically.
`aa_column`	`str`	No	Name of the column containing amino acid positions. Default is 'aa_pos'.
`auto_extract`	`bool`	No	If True, automatically extract uniprot/aa_pos from VEP data when missing. Default is True.
`prefer_database`	`bool`	No	If True, prefer database annotation over VEP parsing when both are available. Default is True.

Return value¶

Returns a new PyMutation object with PFAM domain annotations added as additional columns. Can return None if annotation fails.

Exceptions¶

PfamAnnotationError: if database connection fails or annotation process encounters errors.
ValueError: if required columns are missing or data format is invalid.

Minimal usage example¶

>>> from pyMut.io import read_maf
>>> py_mut = read_maf("mutations_vep_annotated.maf")
>>> annotated = py_mut.annotate_pfam()
>>> print(annotated.data.columns)