def main(): mincols = 1 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 ) if options.mincols: mincols = int( options.mincols ) 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, strand_col = strand_col_1) out_file = open( out_fname, "w" ) for line in merge(g1,mincols=mincols): if type( line ) is GenomicInterval: print >> out_file, "\t".join( line.fields ) elif type( line ) is list: print >> out_file, "\t".join( line ) else: print >> out_file, line
def main(): mincols = 1 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) if options.mincols: mincols = int(options.mincols) 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, strand_col=strand_col_1) out_file = open(out_fname, "w") for line in merge(g1, mincols=mincols): if type(line) is GenomicInterval: print >> out_file, "\t".join(line.fields) elif type(line) is list: print >> out_file, "\t".join(line) else: print >> out_file, line
def main(): mincols = 1 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) if options.mincols: mincols = int(options.mincols) 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) out_file = open(out_fname, "w") try: for line in merge(g1, mincols=mincols): if options.threecol: if type(line) is GenomicInterval: out_file.write( "%s\t%s\t%s\n" % (line.chrom, str(line.startCol), str(line.endCol))) elif type(line) is list: out_file.write("%s\t%s\t%s\n" % (line[chr_col_1], str(line[start_col_1]), str(line[end_col_1]))) else: out_file.write("%s\n" % line) else: if type(line) is GenomicInterval: out_file.write("%s\n" % "\t".join(line.fields)) elif type(line) is list: out_file.write("%s\n" % "\t".join(line)) else: out_file.write("%s\n" % line) except ParseError, exc: out_file.close() fail("Invalid file format: %s" % str(exc))
def main(): mincols = 1 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 ) if options.mincols: mincols = int( options.mincols ) 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 ) out_file = open( out_fname, "w" ) try: for line in merge(g1,mincols=mincols): if options.threecol: if type( line ) is GenomicInterval: out_file.write( "%s\t%s\t%s\n" % ( line.chrom, str( line.startCol ), str( line.endCol ) ) ) elif type( line ) is list: out_file.write( "%s\t%s\t%s\n" % ( line[chr_col_1], str( line[start_col_1] ), str( line[end_col_1] ) ) ) else: out_file.write( "%s\n" % line ) else: if type( line ) is GenomicInterval: out_file.write( "%s\n" % "\t".join( line.fields ) ) elif type( line ) is list: out_file.write( "%s\n" % "\t".join( line ) ) else: out_file.write( "%s\n" % line ) except ParseError, exc: out_file.close() fail( "Invalid file format: %s" % str( exc ) )