'''
deal with this: a seq has multiple blat loci, so it apears multiple times in the bed12. This script rename the seq's name as: seq_trans1 seq_trans2 for each loci
'''
import sys
import getopt
from collections import defaultdict

opts, args = getopt.getopt(sys.argv[1:], 'i:o:')
inBed = ''
outBed = ''

def printErrorMsg():
	sys.stderr.write('Please use -i and -o\n')


for op, value in opts:
	if op == '-i':
		inBed = value
	elif op == '-o':
		outBed = value
	else:
		printErrorMsg()
		sys.exit(1)

if inBed == '' or outBed == '':
	printErrorMsg()
	sys.exit(1)

fBed = open(inBed)
wOut = open(outBed, 'w')

ddSeqLoci = defaultdict(list)
for row in fBed.readlines():
	cols = row.rstrip('\n').split('\t')
	seqName = cols[3]
	ddSeqLoci[seqName].append(cols)

for seqName, loci in ddSeqLoci.items():
	numLoci = len(loci)
	for i in range(numLoci):
		num = i + 1
		locus = loci[i]
		locus[3] = locus[3] + '_trans' + str(num)
		wOut.write('\t'.join(locus) + '\n')

fBed.close()
wOut.close()