SequestOutfile

class pyopenms.SequestOutfile

Bases: object

Cython implementation of _SequestOutfile

Original C++ documentation is available here

Representation of a Sequest output file

__init__()

Overload:

__init__(self) → None

Representation of a Sequest output file

Overload:

__init__(self, in_0: SequestOutfile) → None

Methods

__init__	Overload:
getACAndACType(self, line, accession, ...)	Retrieves the accession type and accession number from a protein description line
getColumns(self, line, substrings, ...)	Retrieves columns from a Sequest outfile line
getSequences
load(self, result_filename, ...)	Loads data from a Sequest outfile

getACAndACType(self, line: bytes | str | String, accession: String, accession_type: String) → None

Retrieves the accession type and accession number from a protein description line

getColumns(self, line: bytes | str | String, substrings: List[bytes], number_of_columns: int, reference_column: int) → bool

Retrieves columns from a Sequest outfile line

getSequences()

load(self, result_filename: bytes | str | String, peptide_identifications: List[PeptideIdentification], protein_identification: ProteinIdentification, p_value_threshold: float, pvalues: List[float], database: bytes | str | String, ignore_proteins_per_peptide: bool) → None

Loads data from a Sequest outfile

Parameters:

• result_filename – The file to be loaded

• peptide_identifications – The identifications

• protein_identification – The protein identifications

• p_value_threshold – The significance level (for the peptide hit scores)

• pvalues – A list with the pvalues of the peptides (pvalues computed with peptide prophet)

• database – The database used for the search

• ignore_proteins_per_peptide – This is a hack to deal with files that use a suffix like “+1” in column “Reference”, but do not actually list extra protein references in subsequent lines