pairwise2_align.py

from Bio import pairwise2
from Bio.Seq import Seq
from Bio import SeqIO
import os
from Bio.SubsMat import MatrixInfo as matlist

filename = 'binding_site_aln.fasta'
def records_to_list(filename):
    records = []
    with open(filename, 'rU') as handle:
        for record in SeqIO.parse(handle, 'fasta'):
            records.append(record)
    return records

def write_pairwise_scores(data, filename):
    with open(filename, 'a') as output:
        output.write(str(data[0]))
        output.write('\t')
        output.write(str(data[1]))
        output.write('\t')
        output.write(str(data[2]))
        output.write('\t')
        output.write('\n')

records = records_to_list(filename)

matrix = matlist.blosum62
matrix['-', '-'] = 0
for char in 'ARNDCQEGHILKMFPSTWYV':
    matrix[char, '-'] = -10
    matrix['-', char] = -10

for record1 in records:
    for record2 in records:
        if record1.id == record2.id:
            align = pairwise2.align.localdx(record1.seq, record2.seq, matrix,
                    score_only=True)
            write_pairwise_scores([record1.id, record2.id, align],
            'pairwise_bs_self_align_output.txt' )