comparison chipsequtil/map_to_known_genes.py @ 14:425c48c48dde draft

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13:89e9a828de51

    for ref_dict in reader :
        gene_ref[ref_dict['chrom']].append(ref_dict)

    return gene_ref

def parse_gene_ref_line(l) :
    l = map(parse_number, l) # coerce to numbers where possible
    l[9] = map(parse_number, l[9].split(',')) # turn 'x,x,x,...' into list
    l[10] = map(parse_number, l[10].split(','))
    return l

if __name__ == '__main__' :

    opts, args = parser.parse_args(sys.argv[1:])

    if len(args) < 3 :
        parser.error('Must provide three filename arguments')

            map_stats['intergenic'] += 1

    if peak_output != sys.stdout:
        print "arrived here."
        peak_output.close()

    #if opts.stats_output != sys.stderr :
    #    opts.stats_output = open(opts.stats_output,'w')

    #for k,v in map_stats.items() :
    #    opts.stats_output.write('%s: %s\n'%(k,v))

    #if opts.stats_output != sys.stderr :
    #    opts.stats_output.close()

14:425c48c48dde

    for ref_dict in reader :
        gene_ref[ref_dict['chrom']].append(ref_dict)

    return gene_ref


def parse_gene_ref_line(l) :
    l = map(parse_number, l) # coerce to numbers where possible
    l[9] = map(parse_number, l[9].split(',')) # turn 'x,x,x,...' into list
    l[10] = map(parse_number, l[10].split(','))
    return l


def main():
    opts, args = parser.parse_args(sys.argv[1:])

    if len(args) < 3 :
        parser.error('Must provide three filename arguments')

            map_stats['intergenic'] += 1

    if peak_output != sys.stdout:
        print "arrived here."
        peak_output.close()
        print "arrived here2."

    #if opts.stats_output != sys.stderr :
    #    opts.stats_output = open(opts.stats_output,'w')

    #for k,v in map_stats.items() :
    #    opts.stats_output.write('%s: %s\n'%(k,v))

    #if opts.stats_output != sys.stderr :
    #    opts.stats_output.close()


if __name__ == '__main__' :
    main()