def main():
parser = khmer_args.build_nodegraph_args()
parser.add_argument("--samples", nargs="+")
parser.add_argument("--save-prefix")
parser.add_argument("--print-tree", action="store_true", default=False)
args = parser.parse_args()
if not args.save_prefix:
print >> sys.stderr, "No save prefix specified! Exiting..."
sys.exit(1)
factory = NodegraphFactory(args)
root = sbt.Node(factory)
for sample_fn in args.samples:
print "*** Build node for", sample_fn
leaf = sbt.Leaf(os.path.basename(sample_fn), os.path.basename(sample_fn), factory.create_nodegraph())
print "--- Consuming file..."
leaf.graph.consume_fasta(sample_fn)
print "--- Adding node to SBT..."
root.add_node(leaf)
print "--- Done with", sample_fn
if args.print_tree:
sbt.print_sbt(root)
print "\n*** Saving to disk"
fn = sbt.save_sbt(root, args.save_prefix)
print "--- Save to", fn
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--sbt-file')
parser.add_argument('--search', nargs='+')
parser.add_argument('--threshold', type=float, default=0.9)
parser.add_argument('--print-tree', action='store_true', default=False)
args = parser.parse_args()
tree = sbt.load_sbt(args.sbt_file)
if args.search:
for fn in args.search:
print '*** Searching', fn
for record in screed.open(fn):
print '---\n', record.name
print [x.metadata for x in tree.find(search_sequence, record.sequence, args.threshold)]
if args.print_tree:
sbt.print_sbt(tree)