for line in itertools.islice(exoresult, 3, None):
if line.startswith('#') or line.startswith(
'Average') or line.startswith('-- completed'):
output.write(line)
else:
cols = line.split('\t')
cols[3] = str(int(cols[3]) + offset)
cols[4] = str(int(cols[4]) + offset)
output.write('\t'.join(cols))
#convert to GFF3 using ExoConverter from EVM
with open(args.out, 'w') as output:
subprocess.call([ExoConverter, exonerate_raw], stdout=output, stderr=FNULL)
#output some quick summary of exonerate alignments that you found
Found = lib.countGFFgenes(exonerate_raw)
lib.log.info('Exonerate finished: found {:,} alignments'.format(Found))
#check for saving output of tblastn
if args.tblastn_out:
shutil.copyfile(BlastResult, args.tblastn_out)
#finally clean-up your mess if failed is empty
if args.debug:
try:
os.rmdir(os.path.join(tmpdir, 'failed'))
empty = True
except OSError:
empty = False
if empty:
lib.SafeRemove(tmpdir)
for file in os.listdir(tmpdir):
if file.endswith('.out'):
with open(os.path.join(tmpdir, file), 'rU') as exoresult:
offset = int(file.split('__')[1])
for line in itertools.islice(exoresult, 3, None):
if line.startswith('#') or line.startswith(
'Average') or line.startswith('-- completed'):
output.write(line)
else:
cols = line.split('\t')
cols[3] = str(int(cols[3]) + offset)
cols[4] = str(int(cols[4]) + offset)
output.write('\t'.join(cols))
#output some quick summary of exonerate alignments that you found
Found = lib.countGFFgenes(args.out)
lib.log.info('Exonerate finished: found {0:,}'.format(Found) + ' alignments')
#check for saving output of tblastn
if args.tblastn_out:
shutil.copyfile(BlastResult, args.tblastn_out)
#finally clean-up your mess if failed is empty
if args.debug:
try:
os.rmdir(os.path.join(tmpdir, 'failed'))
empty = True
except OSError:
empty = False
if empty:
lib.SafeRemove(tmpdir)