##################################
#                                #
# Last modified 7/9/2009         # 
#                                #
# Georgi Marinov                 #
#                                # 
##################################

import sys

try:
	import psyco
	psyco.full()
except:
	pass

def run():

    if len(sys.argv) < 5:
        print 'usage: python %s label inputfilename outfilename newreadlength shift [-color r,g,b]' % sys.argv[0]
        sys.exit(1)

    label = sys.argv[1]
    inputfilename = sys.argv[2]
    outputfilename = sys.argv[3]
    newreadlength = int(sys.argv[4])
    shiftlength = int(sys.argv[5])


    color = '0,0,0'
    if '-color' in sys.argv:
        color = sys.argv[sys.argv.index('-color') + 1]

    outfile = open(outputfilename, 'w')
    outfile.write('track name=%s visibility=4 color=%s\n' % (label, color))

    listoflines = open(inputfilename)
    lineslist = listoflines.readlines()
    lineslist.remove(lineslist[0])
    i=0
    for line in lineslist:
        if i % 1000000 == 0:
            print i, 'reads processed' 
        i+=1
        fields = line.strip().split('\t')
        if len(fields)<6:
            print 'skipping read'
            print line
            continue
        if fields[5]=='+':
            newend=int(fields[1])+newreadlength
            newstart=newend-newreadlength+shiftlength
            newend=newend-shiftlength
            newend=str(newend)
            newstart=str(newstart)
            outline =  '%s\t%s\t%s\t%s\t%s\t%s\t' % (fields[0], newstart, newend, fields[3], fields[4], fields[5])
            outline=outline+'0\t0\t0,0,255\t1\t'+str(newreadlength-1)+'\t0\n'
        if fields[5]=='-':
            newstart=int(fields[2])-newreadlength
            newend=newstart+newreadlength
            newstart=newstart+shiftlength
            newend=newend-shiftlength
            newend=str(newend)
            newstart=str(newstart)
            outline =  '%s\t%s\t%s\t%s\t%s\t%s\t' % (fields[0], newstart, newend, fields[3], fields[4], fields[5])
            outline=outline+'0\t0\t255,0,0\t1\t'+str(newreadlength-1)+'\t0\n'
        outfile.write(outline)
    outfile.close()

run()