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#!/usr/bin/env python
import sys
import os
import random
import numpy
def gen_genome(fh, ref_id, tot_len, per_line=1000):
fh.write('>%s\n' % ref_id)
while tot_len > 0:
ln = min(tot_len, per_line)
assert ln > 0
fh.write(''.join(numpy.random.choice(list('ACGT'), ln)) + '\n')
tot_len -= ln
if __name__ == '__main__':
tot_len = int(sys.argv[1])
tmp_fasta = sys.argv[2]
tmp_idx = sys.argv[3]
bt2_build_exe = sys.argv[4]
num_refs = 1
if len(sys.argv) > 5:
num_refs = int(sys.argv[5])
with open(tmp_fasta, 'w') as fh:
for i in xrange(num_refs):
gen_genome(fh, 'ref%d' % i, tot_len // num_refs)
ret = os.system('%s %s %s' % (bt2_build_exe, tmp_fasta, tmp_idx))
print >> sys.stderr, "Exitlevel: %d" % ret
exit(ret)
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