python keyerror_Python KeyError: '\n'

2015-12-14 08:32:03

0

I use the script below for molecular barcode extraction from fastq files. However, I keep getting the following key error.

File "extractMolecularBarcode.py", line 42, in

dicoBarcode[barcode] += 1

KeyError: '\n'

I know the key error means something is not defined in the dictionary, but I can't figure out the problem. Could you help please? Thank you so much!

Here is the script:

import sys, itertools

iFastq=open(sys.argv[1], 'r')

oFastq=open(sys.argv[2], 'w')

oBarcode=open(sys.argv[3], 'w')

oLigation=open(sys.argv[4], 'w')

dicoBarcode={}

dicoLigation={}

nct='ACTGN'

for barcode in list(itertools.product(nct, repeat=6)):

dicoBarcode["".join(barcode)] = 0

dicoLigation["".join(barcode)] = 0

header= iFastq.readline().rstrip()

while header != '':

totseq= iFastq.readline()

plus = iFastq.readline()

qual = iFastq.readline()

barcode = totseq[0:6]

ligation = totseq[3:9]

seq = totseq[6:]

oFastq.write(header.split(" ")[0]+'_MolecularBarcode:'+barcode+' '+header.split(" ")[1]+'\n')

oFastq.write(seq)

oFastq.write(plus)

oFastq.write(qual[6:])

header= iFastq.readline().rstrip()

dicoBarcode[barcode] += 1

if len(seq) >= 4 :

dicoLigation[ligation] += 1

for barcode, times in dicoBarcode.items():

oBarcode.write("%s\t%s\n" % (barcode, str(times)))

for ligation, times in dicoLigation.items():

oLigation.write("%s\t%s\n" % (ligation, str(times)))