def test_write(self):
"""Reporter: can write to a text file
"""
self._make_working_dir()
reporter = Reporter()
reporter.add("Test Document",title=True)
reporter.add("Lorem ipsum")
report_file = os.path.join(self.wd,"report.txt")
reporter.write(filen=report_file)
self.assertTrue(os.path.isfile(report_file))
expected_contents = """Test Document
=============
Lorem ipsum
"""
self.assertTrue(os.path.exists(report_file))
self.assertEqual(open(report_file,'r').read(),
expected_contents)
def test_write(self):
"""Reporter: can write to a text file
"""
self._make_working_dir()
reporter = Reporter()
reporter.add("Test Document",title=True)
reporter.add("Lorem ipsum")
report_file = os.path.join(self.wd,"report.txt")
reporter.write(filen=report_file)
self.assertTrue(os.path.isfile(report_file))
expected_contents = """Test Document
=============
Lorem ipsum
"""
self.assertTrue(os.path.exists(report_file))
self.assertEqual(open(report_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)
