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(): 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()