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__()