def test_easy_case(self):
""" Test the assembly of the easy case """
f = open(self.fn_easy_case, "r")
solution = "O draconian devil! Oh lame saint!"
for line in f:
reads = line.rstrip().split(";")
contigs = overlap.assemble(reads)
self.assertEqual(contigs[0],solution)
f.close()
log = logging.getLogger("mlearning")
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(
description="""The Da Vyncy assembler """)
parser.add_argument("fn",
help="File with the set of examples to assemble. One example " \
"per line. The fragments need to be separated by ;")
parser.add_argument("--log",
dest="log",
default = False,
help="Log file")
args = parser.parse_args()
if(args.log):
logging.basicConfig(filename=args.log, filemode="w")
else:
logging.basicConfig(stream=sys.stdout)
logging.root.setLevel(logging.ERROR)
f = open(args.fn, "r")
for line in f:
fragments = line.rstrip().split(";")
contigs = overlap.assemble(fragments)
for contig in contigs:
print contig
f.close()
