if __name__=="__main__":
if len(sys.argv)==1:
print "Usage: "+sys.argv[0]+" annotation.tab/bed genomesize *.bed"
print " Find the nearest annotation for given bed."
else:
# check file
if '.tab' in sys.argv[1]:
ftype='gene'
else:
ftype='bed'
# initiation annotations.
annos={}
#for chrom in IO.genomeSize('hg19'):
for chrom in Utils.genomeSize(sys.argv[2]):
if ftype=='bed':
annos[chrom]=BedList()
else:
annos[chrom]=GeneBedList()
# read annotations.
for anno in IO.BioReader(sys.argv[1],ftype=ftype):
if annos.has_key(anno.chrom):
annos[anno.chrom].append(anno)
# sort
for chrom in annos:
annos[chrom].sort()
# Find nearest annoations
p._optionals.title = "Options"
p.add_argument("-i","--input",dest='ifname',type=str,metavar="input.bed",required=True,help="Input file. Can be stdin.")
p.add_argument("-f","--format",dest="ftype",type=str,metavar="bed",default="bed",help="Format of input file. Default is 'bed'. Can be 'bed3', 'bedgraph', 'bed','peak','wig', 'sam2bed' or 'genepred'.")
p.add_argument("-g","--genome",dest='genome',type=str,metavar="Genome",default=None,help="Genome version (hg19, mm10 .etc) or genome size file with chrom and size in each line.")
p.add_argument("-u","--up",dest="up",type=int,metavar="upstream",default=0,help="bps extended to upstream. If minus, trim the 5' end.")
p.add_argument("-d","--down",dest="down",type=int,metavar="downstream",default=0,help="bps extended to downstream. If minus, trim the 3' end.")
p.add_argument("-o","--output",dest="ofname",type=str,metavar="output.bed",default="stdout",help="Output file. Default is stdout.")
if len(sys.argv)==1:
sys.exit(p.print_help())
args = p.parse_args()
return args
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__=="__main__":
# Get parameters
args=argParser()
fh = IO.mopen(args.ofname, 'w')
if args.genome:
genome=Utils.genomeSize(args.genome)
for item in IO.BioReader(args.ifname,args.ftype):
tbed=item.extend(args.up,args.down, args.genome)
print >> fh, tbed
IO.mclose(fh)
