#!/usr/bin/env python3
#
# __init__.py
"""
Comparison between projects and unknowns.
The two submodules, :mod:`~.comparison.projects` and :mod:`~.comparison.unknowns`,
provide identical APIs with different internals to handle reference projects (containing two or more repeats)
and unknown samples (from a single datafile).
.. versionadded:: 0.8.0
"""
#
# Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# 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
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
# OR OTHER DEALINGS IN THE SOFTWARE.
#
# stdlib
from typing import List, Sequence, Tuple, Union
# 3rd party
from pyms.DPA.Alignment import Alignment
from pyms.DPA.PairwiseAlignment import PairwiseAlignment, align_with_tree
# this package
from libgunshotmatch.project import Project
# this package
from . import projects, unknowns
from ._utils import _PaddedPeakList
__all__ = ("align_projects", "get_padded_peak_lists")
# Aliases to prevent clashes with argument names
_projects_mod = projects
_unknowns_mod = unknowns
[docs]def align_projects(
projects: Union[Sequence[Project], Project] = (),
unknowns: Union[Sequence[Project], Project] = (),
D: float = 2.5,
gap: float = 0.3,
) -> Alignment:
"""
Align multiple projects and/or unknowns.
:param projects:
:param unknowns:
:param D: Retention time tolerance for pairwise alignments (in seconds).
:param gap: Gap penalty for pairwise alignments.
:rtype:
.. versionchanged:: 0.9.0
* Added ``D`` and ``gap`` arguments.
* ``projects`` and ``unknowns`` can now be a single :class:`~.Project`.
"""
if isinstance(projects, Project):
projects = [projects]
if isinstance(unknowns, Project):
unknowns = [unknowns]
project_alignments = map(_projects_mod.filter_alignment_to_consolidate, projects)
unknown_alignments = map(_unknowns_mod.filter_alignment_to_consolidate, unknowns)
pwa = PairwiseAlignment([*project_alignments, *unknown_alignments], D=float(D), gap=float(gap))
return align_with_tree(pwa)
[docs]def get_padded_peak_lists(
alignment: Alignment,
projects: Union[Sequence[Project], Project] = (),
unknowns: Union[Sequence[Project], Project] = (),
) -> Tuple[List[_PaddedPeakList], List[_PaddedPeakList]]:
"""
Pad the consolidated peak lists in each project/unknown, from the given between-project alignment.
:param alignment:
:param projects:
:param unknowns:
.. versionchanged:: 0.9.0 ``projects`` and ``unknowns`` can now be a single :class:`~.Project`.
"""
if isinstance(projects, Project):
projects = [projects]
if isinstance(unknowns, Project):
unknowns = [unknowns]
data = alignment.get_peak_alignment(require_all_expr=False, minutes=False)
projects_padded_cp = [_projects_mod.get_padded_peak_list(p, data) for p in projects]
unknowns_padded_cp = [_unknowns_mod.get_padded_peak_list(p, data) for p in unknowns]
return projects_padded_cp, unknowns_padded_cp