#!/usr/bin/python

''''
get bed format from the output of extract_bundle_info
'''

import sys
import os


def line_to_list(line):
    return line.rstrip('\n').split('\t')


def get_usage_instruction(option, desc, value=''):
    return '\t%s\t%s\t%s' % (option, value, desc)


def remove_first_line(reader):
    reader.readline()
    return reader


def get_output_line(l_line):
    return '\t'.join(l_line) + '\n'


def file_to_list(f):
    out_list = []
    with open(f) as reader:
        for line in reader:
            out_list.append(line.rstrip('\n'))
    return out_list


def prepare_dir(d):
    if not os.path.exists(d):
        os.makedirs(d)

def usage(me):
    print 'Usage:\tpython %s  bundle_file bed_file' % me


def modify_start_for_bed(s_start):
    i_start = int(s_start)
    i_start -= 1
    return str(i_start)


def main(bundle_file, bed_file):
    with open(bundle_file) as reader, open(bed_file, 'w') as writer:
        reader = remove_first_line(reader)
        for line in reader:
            l_line = line_to_list(line)
            name, chr, start, end = l_line[:4]
            start = modify_start_for_bed(start)
            out_bed = get_output_line([chr, start, end, name])
            writer.write(out_bed)


if __name__ == '__main__':
    me = sys.argv[0]

    bundle_file = ''
    bed_file = ''
    try:
        bundle_file = sys.argv[1]
        bed_file = sys.argv[2]
    except IndexError:
        usage(me)
        sys.exit(1)

    main(bundle_file, bed_file)