def test_write_counts_file(self):
"""BarcodeCounter: write counts to a file
"""
# Write a file
self._make_working_dir()
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA", lane=1, incr=285302)
bc.count_barcode("TATGCGCGGTG", lane=1, incr=532)
bc.count_barcode("ACCTACCGGTA", lane=1, incr=315)
bc.count_barcode("CCCTTATGCGA", lane=1, incr=22)
bc.count_barcode("ACCTAGCGGTA", lane=2, incr=477)
bc.count_barcode("ACCTCTATGCT", lane=2, incr=368)
bc.count_barcode("ACCCTNCGGTA", lane=3, incr=312)
bc.count_barcode("ACCTTATGCGC", lane=3, incr=248)
counts_file = os.path.join(self.wd, "out.counts")
bc.write(counts_file)
expected_contents = """#Lane Rank Sequence Count
1 1 TATGCGCGGTA 285302
1 2 TATGCGCGGTG 532
1 3 ACCTACCGGTA 315
1 4 CCCTTATGCGA 22
2 1 ACCTAGCGGTA 477
2 2 ACCTCTATGCT 368
3 1 ACCCTNCGGTA 312
3 2 ACCTTATGCGC 248
"""
self.assertTrue(os.path.exists(counts_file))
self.assertEqual(open(counts_file, 'r').read(), expected_contents)
if mismatches is None:
# Set according to barcode lengths found in counts
barcode_length = min(counts.barcode_lengths(lane=lane))
if barcode_length >= 6:
mismatches = 1
else:
mismatches = 0
# Report the analysis
report_barcodes(counts,
lane=lane,
cutoff=cutoff,
sample_sheet=sample_sheet,
mismatches=mismatches,
reporter=reporter)
if opts.report_file is not None:
print "Writing report to %s" % opts.report_file
reporter.write(filen=opts.report_file, title=opts.title)
else:
reporter.write(title=opts.title)
if opts.xls_file is not None:
print "Writing XLS to %s" % opts.xls_file
reporter.write_xls(opts.xls_file, title=opts.title)
if opts.html_file is not None:
print "Writing HTML to %s" % opts.html_file
reporter.write_html(opts.html_file, title=opts.title)
# Output counts if requested
if opts.counts_file_out is not None:
counts.write(opts.counts_file_out)
# Finish
sys.exit(retval)
# Set according to barcode lengths found in counts
barcode_length = min(counts.barcode_lengths(lane=lane))
if barcode_length >= 6:
mismatches = 1
else:
mismatches = 0
# Report the analysis
report_barcodes(counts,
lane=lane,
cutoff=cutoff,
sample_sheet=use_sample_sheet,
mismatches=mismatches,
reporter=reporter,
minimum_read_fraction=args.minimum_read_fraction)
if args.report_file is not None:
print("Writing report to %s" % args.report_file)
reporter.write(filen=args.report_file, title=args.title)
else:
reporter.write(title=args.title)
if args.xls_file is not None:
print("Writing XLS to %s" % args.xls_file)
reporter.write_xls(args.xls_file, title=args.title)
if args.html_file is not None:
print("Writing HTML to %s" % args.html_file)
reporter.write_html(args.html_file, title=args.title)
# Output counts if requested
if args.counts_file_out is not None:
counts.write(args.counts_file_out)
# Finish
sys.exit(retval)