def main():
usage = "%(prog)s [options]"
parser = argparse.ArgumentParser( usage=usage,description=desc,epilog=epilog )
parser.add_argument("-v", dest="verbose", default=False, action="store_true")
parser.add_argument("-i", dest="coords", default=sys.stdin, type=file,
help="coords file name [stdin]")
parser.add_argument("-f", dest="fasta", required=True, type=file,
help="query fasta file" )
parser.add_argument("-o", dest="out", default=sys.stdout, type=argparse.FileType("w"),
help="output base name [stdout]")
o = parser.parse_args()
if o.verbose:
sys.stderr.write( "Options: %s\n" % str(o) )
#load query genome
query2fasta = genome2dict( o.fasta.name )
# load nucmer
matches = nucmer2list( o.coords.name )#; print matches
# sort hits by ref position
sort_hits( matches,query2fasta,o.out,o.verbose )
def main():
usage = "%(prog)s [options]"
parser = argparse.ArgumentParser( usage=usage,description=desc,epilog=epilog )
parser.add_argument("-v", dest="verbose", default=False, action="store_true")
parser.add_argument("-i", dest="coords", default=sys.stdin, type=file,
help="coords file name [stdin]")
parser.add_argument("-f", dest="fasta", required=True, type=file,
help="query fasta file" )
parser.add_argument("-o", dest="out", default=sys.stdout, type=argparse.FileType("w"),
help="output base name [stdout]")
o = parser.parse_args()
if o.verbose:
sys.stderr.write( "Options: %s\n" % str(o) )
#load query genome
query2fasta = genome2dict( o.fasta.name )
# load nucmer
matches = nucmer2list( o.coords.name )#; print matches
# sort hits by ref position
sort_hits( matches,query2fasta,o.out,o.verbose )
def main():
usage = "usage: %prog [options]"
desc = """Order contigs based on nucmer output."""
epilog = """Make sure, coords file is sorted by reference (show-coords -r).
Monoploid number (-x) has to be specified correctly. For details look at: http://en.wikipedia.org/wiki/Ploidy"""
parser = OptionParser( usage=usage,version="%prog 1.0",description=desc,epilog=epilog )
parser.add_option("-o", dest="outfn", default="out",
help="output base name [%default]")
parser.add_option("-i", dest="coords", default="",
help="coords file name [mandatory]")
parser.add_option("-q", dest="query", default="",
help="query file name [mandatory]")
parser.add_option("-r", dest="ref", default="",
help="reference file name [mandatory]")
parser.add_option("-c", dest="qOverlap", default=0.05, type=float,
help="fract of query aligned [%default]")
parser.add_option("-n", dest="haploid", default=2, type=int,
help="haploid number [%default]")
parser.add_option("-x", dest="monoploid", default=2, type=int,
help="monoploid number [%default]")
parser.add_option("-v", dest="verbose", default=False, action="store_true" )
( o, fnames ) = parser.parse_args()
if o.verbose:
sys.stderr.write( "Options: %s\nFastQ files: %s\n" % ( o,fnames ) )
# check input files
for fn in [ o.coords,o.query,o.ref ]:
if not fn:
parser.error( "Provide input file!" )
if not os.path.isfile( fn ):
parser.error( "No such file: %s" % fn )
#load query genome
query2fasta = genome2dict( o.query )
ref2fasta = genome2dict( o.ref )
# load nucmer
matches = nucmer2list( o.coords )
# sort hits by ref position
sort_hits( matches,query2fasta,ref2fasta,o.outfn,o.qOverlap,o.haploid,o.monoploid,o.verbose )
def main():
usage = "usage: %prog [options]"
desc = """Order contigs based on nucmer output."""
epilog = """Make sure, coords file is sorted by reference (show-coords -r).
Monoploid number (-x) has to be specified correctly. For details look at: http://en.wikipedia.org/wiki/Ploidy"""
parser = OptionParser(usage=usage,
version="%prog 1.0",
description=desc,
epilog=epilog)
parser.add_option("-o",
dest="outfn",
default="out",
help="output base name [%default]")
parser.add_option("-i",
dest="coords",
default="",
help="coords file name [mandatory]")
parser.add_option("-q",
dest="query",
default="",
help="query file name [mandatory]")
parser.add_option("-r",
dest="ref",
default="",
help="reference file name [mandatory]")
parser.add_option("-c",
dest="qOverlap",
default=0.05,
type=float,
help="fract of query aligned [%default]")
parser.add_option("-n",
dest="haploid",
default=2,
type=int,
help="haploid number [%default]")
parser.add_option("-x",
dest="monoploid",
default=2,
type=int,
help="monoploid number [%default]")
parser.add_option("-v", dest="verbose", default=False, action="store_true")
(o, fnames) = parser.parse_args()
if o.verbose:
sys.stderr.write("Options: %s\nFastQ files: %s\n" % (o, fnames))
# check input files
for fn in [o.coords, o.query, o.ref]:
if not fn:
parser.error("Provide input file!")
if not os.path.isfile(fn):
parser.error("No such file: %s" % fn)
#load query genome
query2fasta = genome2dict(o.query)
ref2fasta = genome2dict(o.ref)
# load nucmer
matches = nucmer2list(o.coords)
# sort hits by ref position
sort_hits(matches, query2fasta, ref2fasta, o.outfn, o.qOverlap, o.haploid,
o.monoploid, o.verbose)
