##################################
#                                #
# Last modified 05/30/2010       # 
#                                #
# Georgi Marinov                 #
#                                # 
##################################

import sys
import string

def run():

    if len(sys.argv) < 2:
        print 'usage: python %s inputfilename outfilename' % sys.argv[0]
        sys.exit(1)

    inputfilename = sys.argv[1]
    outputfilename = sys.argv[2]

    outfile = open(outputfilename, 'w')

    lineslist = open(inputfilename)
    i=0
    for line in lineslist:
        fields = line.strip().split('\t')
        i+=1
        if i % 100000 == 0:
            print i, 'alignments processed'
        chrom=fields[2]     
        start=int(fields[3])
        stop=int(fields[3])+len(fields[4])
        orientation=fields[1]     
        name=fields[0]     
        source='bowtie'
        score='.'
        group='.'
        frame='.'
        outline = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (chrom, source, name, start, stop, score, orientation, frame, group)
        outfile.write(outline)

    print i, 'alignments processed'
    outfile.close()

run()