Algorithms - Alignment

MST Alignment Module

MST Alignment

Simple Alignment Algorithm

SplineAligner

BorderIntegration

Alignment Datastructures Module

Multipeptide

class msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide

Bases: object

A collection of the same precursors (chromatograms) across multiple runs.

It contains individual precursors that can be accessed by their run id.

all_above_cutoff(cutoff)
all_selected()

Returns True if all peakgroups are selected

find_best_peptide_pg()

Find best peakgroup across all peptides

getAllPeptides()
getPrecursorGroup(runid)

Get precursor group for the given run

:param : :type : param str runid: Run id of the group :param : :type : rtype: PrecursorGroup: Precursor group from the corresponding run

getPrecursorGroups()

Get all precursor groups

Return type:list(PrecursorGroup): All Precursor group from the corresponding run
get_decoy()

Whether the current peptide is a decoy or not

Return type:bool: Whether the peptide is decoy or not
get_id()
get_nr_runs()
get_peptide(runid)
get_peptides()
get_selected_peakgroups()

Get all peakgroups that were selected across all runs and precursor groups

hasPrecursorGroup(runid)

Checks whether a given run has a precursor group

Parameters:runid (str) – Run id to check
Return type:bool: Whether the given run has a precursor group
has_null_peptides()

Whether there are runs in which no peptide was detected (peptide is Null)

Returns:Whether there are Null peptides in this object (not detected in some runs)
Return type:has_null(bool)
has_peptide(runid)
insert(runid, precursor_group)

Insert a PrecursorGroup into the Multipeptide

Parameters:
  • runid (str) – Run id of the group
  • precursor_group (PrecursorGroup) – Precursor group to be inserted
Raises:

Exception – If self.hasPrecursorGroup(runid) is true
more_than_fraction_selected(fraction)
set_nr_runs(v)

MRExperiment

Alignment Helper Module

FDREstimation