def test_assign_barcodes_single_end(self):
"""assign_barcodes_single_end: extract inline barcodes from first 5 bases
"""
nreads = assign_barcodes_single_end(self.fastq_in,
self.fastq_out)
self.assertEqual(nreads,5)
self.assertEqual(open(self.fastq_out,'r').read(),
fastq_r1_out)
def test_assign_barcodes_single_end(self):
"""assign_barcodes_single_end: extract inline barcodes from first 5 bases
"""
nreads = assign_barcodes_single_end(self.fastq_in,
self.fastq_out)
self.assertEqual(nreads,5)
with open(self.fastq_out,'r') as fp:
self.assertEqual(fp.read(),fastq_r1_out)
# assign_barcodes.py: assign barcodes to read headers in fastqs
# Copyright (C) University of Manchester 2016,2019 Peter Briggs
#
"""
assign_barcodes.py
Utility to extract arbitrary sequence fragments from reads in FASTQ
format files and assign these to the index sequence in the read
headers.
"""
import argparse
from auto_process_ngs.fastq_utils import assign_barcodes_single_end
if __name__ == '__main__':
p = argparse.ArgumentParser(
description="Extract arbitrary sequence fragments from reads "
"in INPUT.fq FASTQ file and assign these as the index (barcode) "
"sequences in the read headers in OUTPUT.fq.")
p.add_argument('-n',
action='store',
dest='n',
type=int,
default=5,
help="remove first N bases from each read and assign "
"these as barcode index sequence (default: 5)")
p.add_argument('fq_in', metavar="INPUT.fq", help="Input FASTQ file")
p.add_argument('fq_out', metavar="OUTPUT.fq", help="Output FASTQ file")
args = p.parse_args()
assign_barcodes_single_end(args.fq_in, args.fq_out, args.n)
#!/usr/bin/env python
#
# assign_barcodes.py: assign barcodes to read headers in fastqs
# Copyright (C) University of Manchester 2016 Peter Briggs
#
"""
assign_barcodes.py
Utility to extract arbitrary sequence fragments from reads in FASTQ
format files and assign these to the index sequence in the read
headers.
"""
import optparse
from auto_process_ngs.fastq_utils import assign_barcodes_single_end
if __name__ == '__main__':
p = optparse.OptionParser(usage="%prog [OPTIONS] INPUT.fq OUTPUT.fq",
description="Extract arbitrary sequence "
"fragments from reads in INPUT.fq FASTQ "
"file and assign these as the index "
"(barcode) sequences in the read headers "
"in OUTPUT.fq.")
p.add_option('-n',action='store',dest='n',type='int',default=5,
help="remove first N bases from each read and assign "
"these as barcode index sequence (default: 5)")
opts,args = p.parse_args()
if len(args) != 2:
p.error('Need to specify input and output files')
assign_barcodes_single_end(args[0],args[1],opts.n)
#
"""
assign_barcodes.py
Utility to extract arbitrary sequence fragments from reads in FASTQ
format files and assign these to the index sequence in the read
headers.
"""
import optparse
from auto_process_ngs.fastq_utils import assign_barcodes_single_end
if __name__ == '__main__':
p = optparse.OptionParser(usage="%prog [OPTIONS] INPUT.fq OUTPUT.fq",
description="Extract arbitrary sequence "
"fragments from reads in INPUT.fq FASTQ "
"file and assign these as the index "
"(barcode) sequences in the read headers "
"in OUTPUT.fq.")
p.add_option('-n',
action='store',
dest='n',
type='int',
default=5,
help="remove first N bases from each read and assign "
"these as barcode index sequence (default: 5)")
opts, args = p.parse_args()
if len(args) != 2:
p.error('Need to specify input and output files')
assign_barcodes_single_end(args[0], args[1], opts.n)
