Rewriting the header of fastq

[SeqTrbl]

Hi all,
I need help in re-writting the header of my miseq fastq file. can anyone help please?

Read1:
@130110_A5T23:1:1101:15646:1320:1#0/1
NAGTAAGATACAGTCTATCGGGTTTAAGTTATACAACATAGTACAGTACATTCATACCTACCTCTGCAATTAAATTTGGCGGTGTCATAATGTCTTTCAGCACAACTAAAAGAAAAGTTTAAAAGTGATATAAAGTTATCTTTTGCACTT
+
#>>AABFFFFFFGGGGGGGGGGCFGHHHHHHHHHHHHHHHHGFHHHHHHHHGHGHHHHHHGHHGHHHGHHHHHHHHHEHGGGEEFGHHHHFHHHGHHHHFHHHHGGGHHHHGGHHGHHHHHHHGHBGHHHHHHHHHFHFHHHHHGHFHHH
@130110_A5T23:1:1101:17282:1320:0#0/1
NGGGAGGATGGCTTGAGCCTAGAGGGTTGAGGCTGCAGTGAGCTGTGAGCATGCCATTGCACTCCAGCCTGGGCAACAGAGTGAGGCTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAGAAATAAAATATAAGGGACATAAAATAAAGCAA
+
#>>AAA1A1B>F1A1FAFGCG0GBFEAAEHGBFCFFHHA1FEGGFFGGFFHHHGHHHHGHHHHHHHHHGHGGGHHGHHHFHGHGFGGHHHHHHHHHFGHHGGGEGGGGGGGGGGGCC.<<G0DGGFC:CCC0CC.::00:<00:9C####

Index
@130110_A5T23:1:1101:15646:1320:1#0/2
NTTGTATC
+
#>>AAAFF
@130110_A5T23:1:1101:17282:1320:0#0/2
NTTAGTCT
+
#1>>AAFF

Now Read1 need to be re-written as

@130110_A5T23:1:1101:15646:1320 1:0:1:NTTGTATC
NAGTAAGATACAGTCTATCGGGTTTAAGTTATACAACATAGTACAGTACATTCATACCTACCTCTGCAATTAAATTTGGCGGTGTCATAATGTCTTTCAGCACAACTAAAAGAAAAGTTTAAAAGTGATATAAAGTTATCTTTTGCACTT
+
#>>AABFFFFFFGGGGGGGGGGCFGHHHHHHHHHHHHHHHHGFHHHHHHHHGHGHHHHHHGHHGHHHGHHHHHHHHHEHGGGEEFGHHHHFHHHGHHHHFHHHHGGGHHHHGGHHGHHHHHHHGHBGHHHHHHHHHFHFHHHHHGHFHHH
@130110_A5T23:1:1101:17282:1320 0:0:1:NTTAGTCT
NGGGAGGATGGCTTGAGCCTAGAGGGTTGAGGCTGCAGTGAGCTGTGAGCATGCCATTGCACTCCAGCCTGGGCAACAGAGTGAGGCTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAGAAATAAAATATAAGGGACATAAAATAAAGCAA
+
#>>AAA1A1B>F1A1FAFGCG0GBFEAAEHGBFCFFHHA1FEGGFFGGFFHHHGHHHHGHHHHHHHHHGHGGGHHGHHHFHGHGFGGHHHHHHHHHFGHHGGGEGGGGGGGGGGGCC.<<G0DGGFC:CCC0CC.::00:<00:9C####

i.e. index corresponding to the same id need to come to the header of the Read1 sequences.

Can someone help me out with this??

Thanks and regards

[Jetse]

A python script to help?

Written a small python script which will do it for you, you need python 2.7 or higher to execute.

import sys

def writeNewHeader(head, headIn, out):
    writeSeq = False
    for headLine in headIn:
        if writeSeq == True:
            out.write(head + ":" + headLine)
            return
        if headLine.startswith(head):
            writeSeq = True
            continue

def main(seqFile, headerFile, outFile):
    with open("seq.fastq") as seqIn, open("header.fastq") as headIn,  open("out.fastq", "w") as out:
        for seqLine in seqIn:
            if seqLine.startswith("@"):
                head = seqLine[:-5]
                writeNewHeader(head, headIn, out)
            else:
                out.write(seqLine)
    print "finished!"
    
if len(sys.argv) != 4:
    print "Usage: python renameFastqHeader <sequene File> <header File> <output File>"
else: main(sys.argv[0],sys.argv[1],sys.argv[2])

save code as renameFastqHeader.py, the help will print how to execute it

It is quick and dirty, so don't try to give different files, won't work, and it is not fully optimized... But hope this is what u need