psm_utils.io

psm_utils.io.alphadia

Reader for PSM files from the AlphaDIA search engine.

class psm_utils.io.alphadia.AlphaDIAReader(filename: str | Path, *args: Any, **kwargs: Any)

Reader for AlphaDIA precursor.tsv file.

Parameters:

filename (pathlib.Path) – Path to PSM file.
*args – Additional positional arguments for parent class.
**kwargs – Additional keyword arguments for parent class.

classmethod from_dataframe(dataframe: DataFrame) → PSMList: Create a PSMList from a AlphaDIA Pandas DataFrame.

read_file() → PSMList: Read full PSM file into a PSMList object.

psm_utils.io.cbor

psm_utils.io.diann

psm_utils.io.flashlfq

psm_utils.io.fragpipe

psm_utils.io.idxml

psm_utils.io.ionbot

psm_utils.io.json

psm_utils.io.maxquant

psm_utils.io.msamanda

psm_utils.io.mzid

psm_utils.io.parquet

psm_utils.io.peptide_record

psm_utils.io.pepxml

psm_utils.io.percolator

psm_utils.io.proteome_discoverer

psm_utils.io.proteoscape

psm_utils.io.sage

psm_utils.io.tsv

psm_utils.io.xtandem