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)
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)
mismatches=opts.mismatches,
reporter=reporter)
else:
for lane in lanes:
if lane not in counts.lanes:
logging.error("Requested analysis for lane %d but "
"only have counts for lanes %s" %
(lane,
','.join([str(l) for l in counts.lanes])))
sys.exit(1)
report_barcodes(counts,
lane=lane,
cutoff=cutoff,
sample_sheet=opts.sample_sheet,
mismatches=opts.mismatches,
reporter=reporter)
if opts.report_file is not None:
print "Writing report to %s" % opts.report_file
reporter.write(filen=opts.report_file)
else:
reporter.write()
if opts.xls_file is not None:
print "Writing XLS to %s" % opts.xls_file
reporter.write_xls(opts.xls_file)
if opts.html_file is not None:
print "Writing HTML to %s" % opts.html_file
reporter.write_html(opts.html_file)
# Output counts if requested
if opts.counts_file_out is not None:
counts.write(opts.counts_file_out)
report_barcodes(counts,
cutoff=cutoff,
sample_sheet=opts.sample_sheet,
mismatches=opts.mismatches,
reporter=reporter)
else:
for lane in lanes:
if lane not in counts.lanes:
logging.error("Requested analysis for lane %d but "
"only have counts for lanes %s" %
(lane,
','.join([str(l) for l in counts.lanes])))
sys.exit(1)
report_barcodes(counts,
lane=lane,
cutoff=cutoff,
sample_sheet=opts.sample_sheet,
mismatches=opts.mismatches,
reporter=reporter)
if opts.report_file is not None:
print "Writing report to %s" % opts.report_file
reporter.write(filen=opts.report_file)
else:
reporter.write()
if opts.xls_file is not None:
print "Writing XLS to %s" % opts.xls_file
reporter.write_xls(opts.xls_file)
# Output counts if requested
if opts.counts_file_out is not None:
counts.write(opts.counts_file_out)
