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 = 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)