"""This module defines functions and constants related to sequences."""
import re
__all__ = ['MATCH_SCORE', 'MISMATCH_SCORE', 'GAP_PENALTY',
'GAP_EXT_PENALTY', 'ALIGNMENT_METHOD', 'splitSeqLabel',
'alignBioPairwise']
MATCH_SCORE = 1.0
MISMATCH_SCORE = 0.0
GAP_PENALTY = -1.
GAP_EXT_PENALTY = -0.1
ALIGNMENT_METHOD = 'local'
SPLITLABEL = re.compile(r'[/-]+').split
[docs]def splitSeqLabel(label):
"""Returns label, starting residue number, and ending residue number parsed
from sequence label."""
try:
if label.strip() == '':
raise Exception
idcode, start, end = SPLITLABEL(label)
except Exception:
return label, None, None
else:
try:
return idcode, int(start), int(end)
except Exception:
return label, None, None
[docs]def alignBioPairwise(a_sequence, b_sequence,
ALIGNMENT_METHOD=ALIGNMENT_METHOD,
MATCH_SCORE=MATCH_SCORE, MISMATCH_SCORE=MISMATCH_SCORE,
GAP_PENALTY=GAP_PENALTY, GAP_EXT_PENALTY=GAP_EXT_PENALTY,
max_alignments=1):
"""
Wrapper function to align two sequences using Biopython to support deprecation
and associated warnings.
It first attempts to use :mod:`Bio.Align.PairwiseAligner` and formats the output
to match :mod:`Bio.pairwise2` methods and if it doesn't find it then it defaults
back to :mod:`Bio.pairwise2` methods.
:arg a_sequence: first sequence to align
:type a_sequence: str
:arg b_sequence: second sequence to align
:type b_sequence: str
:arg ALIGNMENT_METHOD: method for pairwise2 alignment
Possible values are ``"local"`` and ``"global"``
:type ALIGNMENT_METHOD: str
:arg MATCH_SCORE: a positive integer, used to reward finding a match
:type MATCH_SCORE: int
:arg MISMATCH_SCORE: a negative integer, used to penalise finding a mismatch
:type MISMATCH_SCORE: int
:arg GAP_PENALTY: a negative integer, used to penalise opening a gap
:type GAP_PENALTY: int
:arg GAP_EXT_PENALTY: a negative integer, used to penalise extending a gap
:type GAP_EXT_PENALTY: int
:arg max_alignments: maximum number of alignments to extract
:type max_alignments: int
"""
import numpy as np
try:
from Bio.Align import PairwiseAligner
aligner = PairwiseAligner()
aligner.mode = ALIGNMENT_METHOD
aligner.match_score = MATCH_SCORE
aligner.mismatch_score = MISMATCH_SCORE
aligner.internal_open_gap_score = GAP_PENALTY
aligner.internal_extend_gap_score = GAP_EXT_PENALTY
alns = aligner.align(a_sequence, b_sequence)
results = []
for i, aln in enumerate(alns):
if i == max_alignments:
break
split_aln = aln.format().split('\n')
if split_aln[0].startswith('target'):
# new biopython
import re
m1 = re.search('[0-9]+', split_aln[0])
begin = m1.group()
m2 = re.search('[0-9]+', split_aln[-4])
m3 = re.search('[0-9]+', split_aln[-4][m2.end():])
end = m3.group()
row_1 = ''.join([line[m1.end()+1:] for line in split_aln[0:-4:4]])
row_1 += split_aln[-4][m2.end()+1:m2.end()+m3.start()-1]
row_2 = ''.join([line[m1.end()+1:] for line in split_aln[2:-4:4]])
row_2 += split_aln[-2][m2.end()+1:m2.end()+m3.start()-1]
else:
begin = split_aln[1].find('|')
end = len(split_aln[1])-1
row_1 = split_aln[0].replace(" ", "-")
row_2 = split_aln[2].replace(" ", "-")
if len(row_1) < len(row_2):
row_1 += "-"*(len(row_2)-len(row_1))
elif len(row_2) < len(row_1):
row_2 += "-"*(len(row_1)-len(row_2))
results.append((row_1, row_2, aln.score, begin, end))
return results
except (ImportError, AttributeError):
from Bio import pairwise2
if ALIGNMENT_METHOD == "local":
return pairwise2.align.localms(a_sequence, b_sequence,
MATCH_SCORE, MISMATCH_SCORE,
GAP_PENALTY, GAP_EXT_PENALTY,
one_alignment_only=1)
elif ALIGNMENT_METHOD == "global":
return pairwise2.align.globalms(a_sequence, b_sequence,
MATCH_SCORE, MISMATCH_SCORE,
GAP_PENALTY, GAP_EXT_PENALTY,
one_alignment_only=1)
else:
raise ValueError("method should be local or global")
