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Source code for galaxy.datatypes.converters.interval_to_bed_converter

#!/usr/bin/env python
# Dan Blankenberg
from __future__ import print_function

import sys

import bx.intervals.io

assert sys.version_info[:2] >= (2, 6)


[docs]def stop_err(msg): sys.stderr.write(msg) sys.exit()
def __main__(): output_name = sys.argv[1] input_name = sys.argv[2] try: chromCol = int(sys.argv[3]) - 1 except Exception: stop_err("'%s' is an invalid chrom column, correct the column settings before attempting to convert the data format." % str(sys.argv[3])) try: startCol = int(sys.argv[4]) - 1 except Exception: stop_err("'%s' is an invalid start column, correct the column settings before attempting to convert the data format." % str(sys.argv[4])) try: endCol = int(sys.argv[5]) - 1 except Exception: stop_err("'%s' is an invalid end column, correct the column settings before attempting to convert the data format." % str(sys.argv[5])) try: strandCol = int(sys.argv[6]) - 1 except Exception: strandCol = -1 try: nameCol = int(sys.argv[7]) - 1 except Exception: nameCol = -1 skipped_lines = 0 first_skipped_line = 0 count = 0 with open(input_name, 'r') as fh, open(output_name, 'w') as out: for count, region in enumerate(bx.intervals.io.NiceReaderWrapper(fh, chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)): try: if nameCol >= 0: name = region.fields[nameCol] else: raise IndexError except Exception: name = "region_%i" % count try: out.write("%s\t%i\t%i\t%s\t%i\t%s\n" % (region.chrom, region.start, region.end, name, 0, region.strand)) except Exception: skipped_lines += 1 if not first_skipped_line: first_skipped_line = count + 1 print("%i regions converted to BED." % (count + 1 - skipped_lines)) if skipped_lines > 0: print("Skipped %d blank or invalid lines starting with line # %d." % (skipped_lines, first_skipped_line)) if __name__ == "__main__": __main__()