def synfind(args):
"""
%prog synfind all.last *.bed
Prepare input for SynFind.
"""
p = OptionParser(synfind.__doc__)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
lastfile = args[0]
bedfiles = args[1:]
fp = open(lastfile)
filteredlast = lastfile + ".filtered"
fw = open(filteredlast, "w")
for row in fp:
b = BlastLine(row)
if b.query == b.subject:
continue
print >> fw, b
fw.close()
logging.debug("Filtered LAST file written to `{0}`".format(filteredlast))
allbed = "all.bed"
fw = open(allbed, "w")
for i, bedfile in enumerate(bedfiles):
prefix = chr(ord('A') + i)
bed = Bed(bedfile)
for b in bed:
b.seqid = prefix + b.seqid
print >> fw, b
fw.close()
logging.debug("Bed file written to `{0}`".format(allbed))
def synfind(args):
"""
%prog synfind all.last *.bed
Prepare input for SynFind.
"""
p = OptionParser(synfind.__doc__)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
lastfile = args[0]
bedfiles = args[1:]
fp = open(lastfile)
filteredlast = lastfile + ".filtered"
fw = open(filteredlast, "w")
for row in fp:
b = BlastLine(row)
if b.query == b.subject:
continue
print(b, file=fw)
fw.close()
logging.debug("Filtered LAST file written to `{0}`".format(filteredlast))
allbed = "all.bed"
fw = open(allbed, "w")
for i, bedfile in enumerate(bedfiles):
prefix = chr(ord('A') + i)
bed = Bed(bedfile)
for b in bed:
b.seqid = prefix + b.seqid
print(b, file=fw)
fw.close()
logging.debug("Bed file written to `{0}`".format(allbed))
