import os
import sys
BIOPYTHON_AVAILABLE = False
try:
from Bio import AlignIO, Alphabet, pairwise2, Seq, SeqIO
BIOPYTHON_AVAILABLE = True
except ImportError:
msg = "Cannot import Biopython - some functionality will not be available." + os.linesep
sys.stderr.write(msg)
[docs]class AlignmentParser(object):
""" Parser for manipulation of MSAs """
[docs] def a3mToTrimmed(self, alnFile, outFile):
"""Convert an .a3m HH-suite file to a FASTA format
:alnFile: A3M format alignment file
:outFile: MSA output file
"""
# A3m is similar to FASTA except indels and lower case letters
records = list(SeqIO.parse(open(alnFile, 'r'), 'fasta'))
records_formatted = self._a3mToTrimmed(records)
SeqIO.write(records_formatted, open(outFile, 'w'), "fasta")
return
def _a3mToTrimmed(self, records):
"""Takes two file handlers"""
for record in records:
record.seq = Seq.Seq(
"".join([c for c in str(record.seq) if not c.islower()]), Alphabet.single_letter_alphabet
)
return records
[docs] def align_sequences(self, seq1, seq2):
"""Global pairwise alignment of two sequences
:returns: aligned sequences as tuple
"""
alignment = pairwise2.align.globalms(seq1, seq2, 2, -1, -0.5, -0.1)
return (alignment[-1][0], alignment[-1][1])
[docs] def resetA3M(self, alnFile, outFile):
""" Reset a A3M alignment to FASTA sequences
Wrapper function for a3mToTrimmed() and removeGaps()
:alnFile: A3M format alignment file
:outFile: FASTA sequence file
"""
records = list(SeqIO.parse(open(alnFile, 'r'), 'fasta'))
records_trimmed = self._a3mToTrimmed(records)
records_trimmed_gapped = self._removeGaps(records)
SeqIO.write(records_trimmed_gapped, open(outFile, 'w'), "fasta")
return
[docs] def read(self, alnFile, alnFormat):
"""Read a multiple sequence alignment
:alnFile: MSA file
:alnFormat: MSA format
:returns: Biopython MSA generator
"""
return AlignIO.parse(open(alnFile, 'r'), alnFormat)
[docs] def removeGaps(self, alnFile, outFile):
""" Remove all gaps in a MSA
:alnFile: FASTA alignment file
:outFile: FASTA sequence file
"""
# Instead of reading an AlignIO object read as SeqIO object to treat them
# straight away as individual sequences
records = list(SeqIO.parse(open(alnFile, 'r'), 'fasta'))
records_formatted = self._removeGaps(records)
SeqIO.write(records_formatted, open(outFile, 'w'), "fasta")
return
def _removeGaps(self, records):
""" Format the string to remove the gaps
"""
for record in records:
record.seq = Seq.Seq(str(record.seq).replace("-", ""), Alphabet.single_letter_alphabet)
return records
[docs] def write(self, alignment, file, format):
"""Write a MSA object to a file"""
AlignIO.write(alignment, open(file, 'w'), format)
return
