def main():
    upstream_pad = 0
    downstream_pad = 0

    options, args = doc_optparse.parse( __doc__ )
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
        in_fname, out_fname = args
    except:
        doc_optparse.exception()
        
    g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
                            chrom_col=chr_col_1,
                            start_col=start_col_1,
                            end_col=end_col_1,
                            strand_col = strand_col_1,
                            fix_strand=True )
    
    try:
        bases = base_coverage(g1)
    except ParseError, exc:
        fail( "Invalid file format: %s" % str( exc ) )
Exemple #2
0
def main():
    upstream_pad = 0
    downstream_pad = 0

    options, args = doc_optparse.parse(__doc__)
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg(
            options.cols1)
        in_fname, out_fname = args
    except:
        doc_optparse.exception()

    g1 = NiceReaderWrapper(fileinput.FileInput(in_fname),
                           chrom_col=chr_col_1,
                           start_col=start_col_1,
                           end_col=end_col_1,
                           strand_col=strand_col_1,
                           fix_strand=True)

    try:
        bases = base_coverage(g1)
    except ParseError, exc:
        fail("Invalid file format: %s" % str(exc))
def main():

    upstream_pad = 0
    downstream_pad = 0

    options, args = cookbook.doc_optparse.parse( __doc__ )
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
        in_fname, out_fname = args
    except:
        cookbook.doc_optparse.exception()

    g1 = GenomicIntervalReader( fileinput.FileInput( in_fname ),
                                chrom_col=chr_col_1,
                                start_col=start_col_1,
                                end_col=end_col_1)
    if strand_col_1 >= 0:
        g1.strand_col=strand_col_1

    out_file = open( out_fname, "w" )

    bases = base_coverage(g1)
    print >> out_file, str(bases)
def main():

    upstream_pad = 0
    downstream_pad = 0

    options, args = cookbook.doc_optparse.parse(__doc__)
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg(
            options.cols1)
        in_fname, out_fname = args
    except:
        cookbook.doc_optparse.exception()

    g1 = GenomicIntervalReader(fileinput.FileInput(in_fname),
                               chrom_col=chr_col_1,
                               start_col=start_col_1,
                               end_col=end_col_1)
    if strand_col_1 >= 0:
        g1.strand_col = strand_col_1

    out_file = open(out_fname, "w")

    bases = base_coverage(g1)
    print >> out_file, str(bases)