quick and dirty script to create a barcode read fastq file from a sequence read fastq file with barcodes in the headers

README.md

USAGE: extract_fastq_barcodes_from_header.py input_reads.fastq barcode_reads.fastq

extract_fastq_barcodes_from_header.py

#!/usr/bin/env python
# File created on 16 Nov 2012
from __future__ import division

__author__ = "Greg Caporaso"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.5.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Development"

from sys import argv
from unittest import TestCase, main as test_main

def script_main(input_f):
    for line in input_f:
        if line.startswith('@'):
            header = line.strip()
            barcode = header.split(':')[-1]
            yield '%s\n%s\n+\nbbbbbbbbbbbb' % (header,barcode)
        else:
            pass

class ScriptTests(TestCase):
    
    def setUp(self):
        self.fake_file = fake_file.split('\n')
        self.expected_output = expected_output
    
    def test_main(self):
        """ expected barcode fastq is generated """
        self.assertEqual('\n'.join(script_main(self.fake_file)),
                         self.expected_output)

fake_file = """@M141:79:749142:1:1101:16224:1417 1:N:0:CGACTAATGTGT
TACGTAGGTGGCAAGCGTTAGCCGGAATTATTGGGCGTAAAGCGCGAGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGACACTGTAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTAGCTAAGTCTACTTTCTGGACTGTAACTGACGCTGAGCTGCGACAGCGTGGGGATCAAACA
+
=9<==>9+--,55<@@EEEC+8AC+CCE-AAA.ACCCCCDAFFEAC>C555--*55<+55C+DDEDE3=C==4444+44@D@A33<@D@DE)@0@############################################################################################################################################################
@M141:79:749142:1:1101:16633:1423 1:N:0:CGACTTATGTGA
TACGTAGGTGGCAAGCGTTATCCGGAAGTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCTGTGACATGCGCAGAGATATGGAGACACACCAGTGGCGAAGGCGACGTTCTGGTCTGTAACTGACGCTGATGTGCACAAGCGTGGGGATCACACA
+
,5<==>>+<@@<@<@@E6+>+AACA=C+8ADAF=EE7>CEEF@ECCD>5>CEEDACCD5<CE@EDEEEEEDE@@@:+4@DDD==@@:2;@98@8::2296<E(;;6<EE<E;(66;(/;?66;<;<<E;?/.///96<EEE(6;?<?=E######################################################################################################
@M141:79:749142:1:1101:15549:1428 1:N:0:CGACTTATGTGT
TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTGTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTTGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACATCAGTGGCGAAGGCGACTTGCTCGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGTGATCCATCA
+
5<???BB?B?<5?B,<CC6CC8ECCEAFBEAA09A7>C>CCFG:D7>C>>>E=CD<<5+4CFFFFDFCDFFFF?@D,4DFD@@>>@DDEEE<A;<***1:;B;;?ACAEA?*0:*0?CC//::0A:AACA*008?EE8::::??/:0:A??AAC?################################################################################################
@M141:79:749142:1:1101:16736:1437 1:N:0:CGACTTATGTAT
TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTCGCGGTGAAATGCGCAGAGATATGGAGGCACACCAGTGGCGAAGGCGACCTACTGGTCTGTTACTGACGCTGATGTGCGCAAGCTAGAGGATCAAACA
+
<???,5?9BB9<?-ABC@>C;CFA=CEHHHFFFGHF+>CEHHHHHHHHHHAEHH7CCD+DCCCFHDDBD@444B,??DFFFEEEEEEE,;C@B;:B**28AEEE*C:*0:?:*0:AECAE*0??E*00*:?**0/*0**0?EEECEEC:A:*/*08'2?')00??EAA?820:A#############################################################################
"""

expected_output = """@M141:79:749142:1:1101:16224:1417 1:N:0:CGACTAATGTGT
CGACTAATGTGT
+
bbbbbbbbbbbb
@M141:79:749142:1:1101:16633:1423 1:N:0:CGACTTATGTGA
CGACTTATGTGA
+
bbbbbbbbbbbb
@M141:79:749142:1:1101:15549:1428 1:N:0:CGACTTATGTGT
CGACTTATGTGT
+
bbbbbbbbbbbb
@M141:79:749142:1:1101:16736:1437 1:N:0:CGACTTATGTAT
CGACTTATGTAT
+
bbbbbbbbbbbb
"""

if __name__ == "__main__":
    
    if len(argv) == 1:
        print "USAGE: extract_fastq_barcodes_from_header.py input_reads.fastq barcode_reads.fastq"
        print "\nTest output:\n"
        test_main()
    else:
        output_f = open(argv[2],'w')
        for rec in script_main(open(argv[1],'U')):
            output_f.write(rec)
            output_f.write('\n')
        output_f.close()