MAF annotation

wrap_maf_vep_annotate_protein¶

Short description¶

Annotates a MAF file with protein-level VEP information and automatically merges the VEP output back into the original MAF, producing an annotated file ready for downstream analysis.

Signature¶

def wrap_maf_vep_annotate_protein(
    maf_file: Union[str, Path],
    cache_dir: Union[str, Path],
    fasta: Union[str, Path],
    output_file: Optional[Union[str, Path]] = None,
    synonyms_file: Optional[Union[str, Path]] = None,
    assembly: Optional[str] = None,
    version: Optional[str] = None,
    compress: bool = True,
    no_stats: bool = True
) -> Tuple[bool, str]:

Parameters¶

Parameter	Type	Required	Description
`maf_file`	`str` \| `Path`	Yes	Path to the input MAF file (`.maf` or `.maf.gz`).
`cache_dir`	`str` \| `Path`	Yes	Directory containing the local VEP cache.
`fasta`	`str` \| `Path`	Yes	Reference FASTA used by VEP.
`output_file`	`str` \| `Path`	No	Destination for the raw VEP output. If omitted, a directory named `vep_annotation_<timestamp>` is created beside the MAF.
`synonyms_file`	`str` \| `Path`	No	Chromosome–synonyms file. When `None`, it is inferred from the cache directory.
`assembly`	`str`	No	Genome assembly (e.g. `"GRCh38"`). If omitted, parsed from `cache_dir`.
`version`	`str`	No	VEP cache version (e.g. `"113"`). If omitted, parsed from `cache_dir`.
`compress`	`bool`	No	Gzip-compress the merged MAF (`True`, default).
`no_stats`	`bool`	No	Run VEP with `--no_stats` to skip statistics (`True`, default).

Return value¶

Tuple[bool, str] where

bool – True on successful VEP run (merge may still fail) and False on fatal error.
str – Path(s) to the VEP output and (when merge succeeds) the final annotated MAF. Never None.

Exceptions¶

ValueError – if cache_dir name does not encode assembly/version and they are not provided.
FileNotFoundError – if maf_file, cache_dir, or fasta does not exist.

Minimal usage example¶

```python from pathlib import Path from vep_annotate import wrap_maf_vep_annotate_protein

success, info = wrap_maf_vep_annotate_protein( maf_file="tumor_samples.maf.gz", cache_dir=Path("/data/vep_cache"), fasta=Path("/data/genome/GRCh38.fa") ) print(success, info) ````