#!/usr/bin/env python3
#
# unknown.py
"""
Comparison between project(s) and unknowns.
"""
#
# Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
#
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# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# 3rd party
import pandas # type: ignore[import-untyped]
from pyms.DPA.Alignment import Alignment
# this package
from libgunshotmatch.project import Project
from libgunshotmatch.utils import create_alignment
# this package
from ._utils import _get_padded_peak_list, _PaddedPeakList
__all__ = ("filter_alignment_to_consolidate", "get_padded_peak_list")
[docs]def filter_alignment_to_consolidate(unknown: Project) -> Alignment:
"""
Filter peaks from an unknown's ``alignment`` to only those which survived the ``consolidate`` process.
:param unknown:
"""
assert unknown.consolidated_peaks is not None
cp_rts = [cp.rt for cp in unknown.consolidated_peaks]
aligned_peaks = [peak for peak in unknown.alignment.peakpos[0] if peak.rt in cp_rts]
# Sanity check
for c_expr_peaks, expr_peaks in zip([aligned_peaks], unknown.alignment.peakpos):
for peak in c_expr_peaks:
assert peak in expr_peaks
# Create new Alignment object
return create_alignment([aligned_peaks], [unknown.name])
[docs]def get_padded_peak_list(unknown: Project, alignment_rts: pandas.DataFrame) -> _PaddedPeakList:
"""
Returns a list of consolidated peaks for the unknown sample, based on the between-project alignment.
:param unknown:
:param alignment_rts: Pandas DataFrame giving retention times for the peak alignment.
The output of :meth:`~pyms.DPA.Alignment.Alignment.get_peak_alignment`.
"""
rts = list(alignment_rts[unknown.name])
return _get_padded_peak_list(unknown, rts)