Algorithms - Alignment¶
Alignment Datastructures Module¶
Multipeptide¶
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class
msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide¶ A collection of the same precursors (chromatograms) across multiple runs.
It contains individual precursors that can be accessed by their run id.
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all_above_cutoff(cutoff)¶
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all_selected()¶ Returns True if all peakgroups are selected
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find_best_peptide_pg()¶ Find best peakgroup across all peptides
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getAllPeptides()¶
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getPrecursorGroup(runid)¶ Get precursor group for the given run
- Args:
- runid (str): Run id of the group
- Returns:
- precursor_group (
PrecursorGroup): Precursor group from the corresponding run
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getPrecursorGroups()¶ Get all precursor groups
- precursor_group: list of
PrecursorGroup - All Precursor group from the corresponding run
- precursor_group: list of
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get_decoy()¶ Whether the current peptide is a decoy or not
- Returns:
- decoy(bool): Whether the peptide is decoy or not
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get_id()¶
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get_nr_runs()¶
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get_peptide(runid)¶
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get_peptides()¶
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get_selected_peakgroups()¶ Get all peakgroups that were selected across all runs and precursor groups
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hasPrecursorGroup(runid)¶ Checks whether a given run has a precursor group
- Args:
- runid (str): Run id to check
- check : bool
- Whether the given run has a precursor group
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has_null_peptides()¶ Whether there are runs in which no peptide was detected (peptide is Null)
- Returns:
- has_null(bool): Whether there are Null peptides in this object (not detected in some runs)
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has_peptide(runid)¶
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insert(runid, precursor_group)¶ Insert a
PrecursorGroupinto the Multipeptide- Args:
- runid(str): Run id of the group
precursor_group(
PrecursorGroup): Precursor group to be inserted - Raises:
- Exception: If self.hasPrecursorGroup(runid) is true
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more_than_fraction_selected(fraction)¶
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set_nr_runs(v)¶
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