def main():
options, args = doc_optparse.parse(__doc__)
try:
sources = args[0].translate(tree_tx).split()
seq_db = load_seq_db(args[1])
index = maf.MultiIndexed(args[2:])
out = maf.Writer(sys.stdout)
missing_data = bool(options.missingData)
use_strand = bool(options.strand)
except:
doc_optparse.exception()
for line in sys.stdin:
fields = line.split()
ref_src, start, end = fields[0:3]
if use_strand and len(fields) > 5:
strand = fields[5]
else:
strand = '+'
do_interval(sources, index, out, ref_src, int(start), int(end), seq_db,
missing_data, strand)
out.close()
def main():
options, args = doc_optparse.parse( __doc__ )
try:
sources = args[0].translate( tree_tx ).split()
seq_db = load_seq_db( args[1] )
index = maf.MultiIndexed( args[2:] )
out = maf.Writer( sys.stdout )
missing_data = bool(options.missingData)
use_strand = bool(options.strand)
except:
doc_optparse.exception()
for line in sys.stdin:
fields = line.split()
ref_src, start, end = fields[0:3]
if use_strand and len( fields ) > 5:
strand = fields[5]
else:
strand = '+'
do_interval( sources, index, out, ref_src, int( start ), int( end ), seq_db, missing_data, strand )
out.close()