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#!/usr/bin/python3
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import os
import stat
import sys
import shutil
def read_fasta(filename):
"""
Returns list of FASTA entries (in tuples: name, seq)
"""
res_name = []
res_seq = []
first = True
seq = ''
for line in open(filename):
if line[0] == '>':
res_name.append(line.strip())
if not first:
res_seq.append(seq)
else:
first = False
seq = ''
else:
seq += line.strip()
res_seq.append(seq)
return zip(res_name, res_seq)
def simulate_by_fasta(fasta, read_length, filename):
outfile = open(filename, 'w')
ideal = ''.join(['I' for i in range(0, read_length)])
n = 0
for name, seq in fasta:
for i in xrange(0, len(seq) - read_length - 1):
outfile.write('@' + name[1:] + '_' + str(n) + '_' + str(i) + '\n')
outfile.write(seq[i : i + read_length] + '\n')
outfile.write('+' + name[1:] + '_' + str(n) + '_' + str(i) + '\n')
outfile.write(ideal + '\n')
n += 1
outfile.close()
simulate_by_fasta(read_fasta(sys.argv[1]), int(sys.argv[2]), sys.argv[3])
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