Try this python script:

import sys

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

header = ''
data = ''

outFile = {}

for line in inFile:
    if line[0] == "@":
        if header != '':
            barcode = header.split('#')[-1].split('/')[0]
            if not outFile.has_key(barcode):
                outFile[barcode] = open(barcode + ".fastq",'a')

            outFile[barcode].write(header + "\n" + data)

        header = line.strip()
        data = ''
    else:
        data += line

barcode = header.split('#')[-1].split('/')[0]
if not outFile.has_key(barcode):
    outFile[barcode] = open(barcode + ".fastq",'a')

outFile[barcode].write(header + "\n" + data)

Save as yourName.py. Use by: python yourName.py file.fastq. You might have to mess with the barcode parsing code. Right now, it parses the barcode by taking anything between the last '#' and "/" character. It should work if there is no "/" character also.

Fastq-tools allows you to grep sequence identifiers:

fastq-grep -i AGTTCC mysequence.fq > AGTTCC_seqs.fq

The following perl 1-liner will split its standard input into newly created files named after the its input file and the barcodes appearing on its standard input.

perl -p -e 'open(STDOUT,">>","$1_$ARGV") if m|^@.*\#([ATGC]+)\/\d+|' your.fastq

will split your.fastq into files named, i.e.

• AGTTCC_your.fastq
• AGAGGA_your.fastq
• etc, based on its input.

You could use the awk program below to generate a fastq file that has the barcodes appended to each sequence (and quality string). Put the awk code into prog.awk then run it as:

awk -f prog.awk < data.fq

Here is the awk file:

/^@HWI-ST/ {
    # extract the barcode as the sequence stored
    # between # and /
    split($0,parts,"#")
    split(parts[2], code, "/")
    barcode = code[1] 
    print 
    next;
}

/^+$/ {
    print
    next
}

{
    print barcode "" $0
}

You can do this with Biopieces:

read_fastq -i test.fq |                      # read in the fastq entries
split_vals -k SEQ_NAME -d '#' |              # split the sequence name on #
split_vals -k SEQ_NAME_1 -d '/' -K BARCODE | # split again on / to get the barcode
write_fastq_files -d Files -k BARCODE -x     # write files in Files dir using barcodes as names

Hey, look at here: http://www.keepautomation.com/products/net_barcode/ I found this web by chance, it will tell you every detail on barcode. Hope you'll find your answer.