alphabase.psm_reader.dia_psm_reader

Readers for Spectronaut’s output library and reports, Swath data and DIANN data.

Classes:

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

Reader for DIANN data.

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

Reader for Spectronaut's output library TSV/CSV.

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

Reader for Spectronaut's report TSV/CSV.

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

Reader for SWATH or OpenSWATH library TSV/CSV.

Functions:

register_readers()

Register readers for Spectronaut's output library and reports, Swath data and DIANN data.
class alphabase.psm_reader.dia_psm_reader.DiannReader(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, mod_seq_columns: List[str] | None = None, fdr: float = 0.01, keep_decoy: bool = False, rt_unit: str | None = None, filter_first_search_fdr: bool = False, filter_second_search_fdr: bool = False, **kwargs)[source][source]

Bases: ModifiedSequenceReader

Reader for DIANN data.

Methods:

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

Reader for DIANN data.
__init__(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, mod_seq_columns: List[str] | None = None, fdr: float = 0.01, keep_decoy: bool = False, rt_unit: str | None = None, filter_first_search_fdr: bool = False, filter_second_search_fdr: bool = False, **kwargs)[source][source]

Reader for DIANN data.

See documentation of PSMReaderBase for more information.

Parameters:

  • filter_first_search_fdr (bool, optional) – If True, the FDR filtering will be done also to the first search columns (fdr1_search1 and fdr2_search1)

  • filter_second_search_fdr (bool, optional) – If True, the FDR filtering will be done also to the second columns (fdr1_search2 and fdr2_search2)

  • parameters. (See documentation of PSMReaderBase for the rest of)

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

Bases: ModifiedSequenceReader

Reader for Spectronaut’s output library TSV/CSV.

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

Bases: ModifiedSequenceReader

Reader for Spectronaut’s report TSV/CSV.

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

Bases: SpectronautReader

Reader for SWATH or OpenSWATH library TSV/CSV.

alphabase.psm_reader.dia_psm_reader.register_readers() → None[source][source]

Register readers for Spectronaut’s output library and reports, Swath data and DIANN data.