DLOOPplus = range(15800,16570) + range(1,1500)
dloops_fn = os.path.join(here, 'dloops.fasta')
ofn = os.path.join(here, 'fail_dloop.txt')
fail_fn = os.path.join(here, 'dloop_expect_to_fail.txt')
expect_to_fail = []
for line in open(fail_fn, 'U'):
expect_to_fail.append(int(line.strip()[:-1]))
of = open(ofn, 'w')
count = 0
for entry in fasta(dloops_fn):
count += 1
if count not in expect_to_fail:
try:
sites = seq2sites(entry["sequence"])
seq = sites2seq(sites, region=DLOOPplus)
seq = seq.replace('-', '')
if entry["sequence"] in seq:
print count, entry["name"], sites2str(sites)
else:
print 'FAILED', count, entry["name"]
of.write('%d, %s\n' % (count, entry["name"]))
except Exception, e:
print 'FAILED',e, count, entry["name"]
of.write('%d, %s\n' % (count, entry["name"]))
of.flush()
of.close()