alphabase.psm_reader.pfind_reader

pFind reader.

Functions:

get_pFind_mods(pfind_mod_str)	Parse pFind modification string.
parse_pfind_protein(protein, *[, keep_reverse])	Parse pFind protein string.
register_readers()	Register pFind readers.
translate_pFind_mod(mod_str)	Translate pFind modification string.

Classes:

pFindReader(*[, column_mapping, ...])

Reader for pFind's .txt files.

alphabase.psm_reader.pfind_reader.get_pFind_mods(pfind_mod_str: str) → Tuple[str, str]

Parse pFind modification string.

class alphabase.psm_reader.pfind_reader.pFindReader(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, fdr: float = 0.01, keep_decoy: bool = False, rt_unit: str | None = None, mod_seq_columns: List[str] | None = None, **kwargs)

Bases: PSMReaderBase

Reader for pFind’s .txt files.

alphabase.psm_reader.pfind_reader.parse_pfind_protein(protein: str, *, keep_reverse: bool = True) → str

Parse pFind protein string.

alphabase.psm_reader.pfind_reader.register_readers() → None

Register pFind readers.

alphabase.psm_reader.pfind_reader.translate_pFind_mod(mod_str: str) → str | NAType

Translate pFind modification string.