Exemplo n.º 1
0
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
Exemplo n.º 2
0
    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)