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)