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)