def main():
start_time = time()
args = parse_args()
if not os.path.exists(args.outdir):
os.mkdir(args.outdir)
os.chmod(args.outdir, 0o775)
print 'Converting motifs...'
sys.stdout.write('Motif is ')
if args.type == 'iupac':
print 'IUPAC'
meme = parse_iupac(args.motif, args.outdir)
elif args.type == 'matrix':
print 'matrix'
matrix = [map(float, x.split()) for x in args.motif.splitlines()]
meme = meme_util.create_meme(matrix, os.path.join(args.outdir, 'input'))
print 'Running TOMTOM...'
print 'Parameters:'
print ' -thresh %.2f' % (args.thresh)
if args.evalue:
print ' -evalue'
print ' -min-overlap %d' % (args.min_overlap)
print 'Looking among %s motifs' % ('central' if args.central else 'all')
sys.stdout.flush()
run_tomtom(meme, args.outdir, args.central, args.thresh, args.min_overlap, args.evalue)
print 'Done in %.2fs' % (time() - start_time)
sys.stdout.flush()
def main():
try:
args = parse_args()
except argparse.ArgumentError as ae:
print json.dumps({'name': ae.message.capitalize(), 'file': None})
sys.exit(1)
pspm = json.loads(urllib2.unquote(args.matrix))
if not os.path.exists(args.outdir):
os.mkdir(args.outdir)
os.chmod(args.outdir, 0o775)
meme_fname = create_meme(pspm, os.path.join(args.outdir, 'input'))
exit_status = run_tomtom(meme_fname, args.outdir,
args.db, args.th, args.evalue, args.min_overlap)
if exit_status == 0:
print json.dumps({'name': 'TOMTOM results',
'file': os.path.relpath(os.path.join(args.outdir, 'tomtom.html'), config.base_path)})
else:
print json.dumps({'name': ('An error occured (ERROR %d)'
'. Please report this error with the following code: <code>%s</code>') % \
(exit_status, os.path.basename(args.outdir)), 'file': None})
def main():
try:
args = parse_args()
except argparse.ArgumentError as ae:
print json.dumps({'name': ae.message.capitalize(), 'file': None})
sys.exit(1)
pspm = json.loads(urllib2.unquote(args.matrix))
if not os.path.exists(args.outdir):
os.mkdir(args.outdir)
os.chmod(args.outdir, 0o775)
meme_fname = create_meme(pspm, os.path.join(args.outdir, 'input'))
exit_status = run_tomtom(meme_fname, args.outdir, args.db, args.th,
args.evalue, args.min_overlap)
if exit_status == 0:
print json.dumps({
'name':
'TOMTOM results',
'file':
os.path.relpath(os.path.join(args.outdir, 'tomtom.html'),
config.base_path)
})
else:
print json.dumps({'name': ('An error occured (ERROR %d)'
'. Please report this error with the following code: <code>%s</code>') % \
(exit_status, os.path.basename(args.outdir)), 'file': None})
def main():
start_time = time()
args = parse_args()
if not os.path.exists(args.outdir):
os.mkdir(args.outdir)
os.chmod(args.outdir, 0o775)
print 'Converting motifs...'
sys.stdout.write('Motif is ')
if args.type == 'iupac':
print 'IUPAC'
meme = parse_iupac(args.motif, args.outdir)
elif args.type == 'matrix':
print 'matrix'
matrix = [map(float, x.split()) for x in args.motif.splitlines()]
meme = meme_util.create_meme(matrix,
os.path.join(args.outdir, 'input'))
print 'Running TOMTOM...'
print 'Parameters:'
print ' -thresh %.2f' % (args.thresh)
if args.evalue:
print ' -evalue'
print ' -min-overlap %d' % (args.min_overlap)
print 'Looking among %s motifs' % ('central' if args.central else 'all')
sys.stdout.flush()
run_tomtom(meme, args.outdir, args.central, args.thresh, args.min_overlap,
args.evalue)
print 'Done in %.2fs' % (time() - start_time)
sys.stdout.flush()
def main():
args = parse_args()
pspm = json.loads(urllib2.unquote(''.join(sys.stdin).decode('utf-8')))
meme = create_meme(pspm, '%s_%d' % (args.id, time()))
out_dir = os.path.join(config.tmp_dir, '%s_%d' % (args.id, time()))
if not os.path.exists(out_dir):
os.mkdir(out_dir)
os.chmod(out_dir, 0o775)
with open(run_meme2images(meme, args.format, out_dir)) as f:
print f.read()
def main():
args = parse_args()
pspm = json.loads(urllib2.unquote(''.join(sys.stdin).decode('utf-8')))
meme = create_meme(pspm, '%s_%d' % (args.id, time()))
out_dir = os.path.join(config.tmp_dir, '%s_%d' % (args.id, time()))
if not os.path.exists(out_dir):
os.mkdir(out_dir)
os.chmod(out_dir, 0o775)
with open(run_meme2images(meme, args.format, out_dir)) as f:
print f.read()