def gff(args):
"""
%prog gff pslfile
Convert to gff format.
"""
p = OptionParser(gff.__doc__)
p.add_option("--source", default="GMAP",
help="specify GFF source [default: %default]")
p.add_option("--type", default="EST_match",
help="specify GFF feature type [default: %default]")
p.add_option("--suffix", default=".match",
help="match ID suffix [default: \"%default\"]")
p.add_option("--swap", default=False, action="store_true",
help="swap query and target features [default: %default]")
p.add_option("--simple_score", default=False, action="store_true",
help="calculate a simple percent score [default: %default]")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
pslfile, = args
fw = must_open(opts.outfile, "w")
print >> fw, "##gff-version 3"
psl = Psl(pslfile)
for p in psl:
if opts.swap:
p.swap
psl.trackMatches(p.qName)
# switch from 0-origin to 1-origin
p.qStart += 1
p.tStart += 1
if p.strand == "-":
p.qStart, p.qEnd = p.qEnd, p.qStart
print >> fw, p.gffline(source=opts.source, type=opts.type, suffix=opts.suffix, \
primary_tag="ID", alt_score=opts.simple_score, \
count=psl.getMatchCount(p.qName))
# create an empty PslLine() object and load only
# the targetName, queryName and strand info
part = PslLine("\t".join(str(x) for x in [0] * p.nargs))
part.tName, part.qName, part.strand = p.tName, p.qName, p.strand
nparts = len(p.qStarts)
for n in xrange(nparts):
part.qStart, part.tStart, aLen = p.qStarts[n], p.tStarts[n], p.blockSizes[n]
part.qEnd = part.qStart + aLen
part.tEnd = part.tStart + aLen
part.qStart += 1
part.tStart += 1
if part.strand == "-":
part.aLen = p.blockSizes[nparts - 1 - n]
part.qEnd = p.qStarts[nparts - 1 - n]
part.qStart = part.qEnd + part.aLen
part.qEnd += 1
print >> fw, part.gffline(source=opts.source, suffix=opts.suffix, \
count=psl.getMatchCount(part.qName))
