def test_add(self):
"""Reporter: can add content
"""
reporter = Reporter()
self.assertEqual(len(reporter),0)
self.assertFalse(reporter)
self.assertEqual(str(reporter),"")
reporter.add("Title text",title=True)
reporter.add("Some words")
self.assertEqual(len(reporter),2)
self.assertTrue(reporter)
self.assertEqual(str(reporter),
"""Title text
==========
Some words""")
def test_write_xls(self):
"""Reporter: can write to an XLS file
"""
self._make_working_dir()
reporter = Reporter()
reporter.add("Test Document",title=True)
reporter.add("Lorem ipsum")
report_xls = os.path.join(self.wd,"report.xls")
reporter.write_xls(report_xls)
self.assertTrue(os.path.isfile(report_xls))
def test_write_xls(self):
"""Reporter: can write to an XLS file
"""
self._make_working_dir()
reporter = Reporter()
reporter.add("Test Document",title=True)
reporter.add("Lorem ipsum")
report_xls = os.path.join(self.wd,"report.xls")
reporter.write_xls(report_xls)
self.assertTrue(os.path.isfile(report_xls))
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)
def test_add(self):
"""Reporter: can add content
"""
reporter = Reporter()
self.assertEqual(len(reporter),0)
self.assertFalse(reporter)
self.assertEqual(str(reporter),"")
reporter.add("Title text",title=True)
reporter.add("Some words")
self.assertEqual(len(reporter),2)
self.assertTrue(reporter)
self.assertEqual(str(reporter),
"""Title text
==========
Some words""")
# Read counts from counts file(s)
counts = BarcodeCounter(*args)
elif len(args) == 1 and os.path.isdir(args[0]):
# Generate counts from bcl2fastq output
counts = count_barcodes_bcl2fastq(args[0])
else:
# Generate counts from fastq files
counts = count_barcodes(args)
# Deal with cutoff
if opts.cutoff == 0.0:
cutoff = None
else:
cutoff = opts.cutoff
# Report the counts
if not opts.no_report:
reporter = Reporter()
if lanes is None:
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,
def test_write_html(self):
"""Reporter: can write to a HTML file
"""
self._make_working_dir()
reporter = Reporter()
reporter.add("This is a Test",title=True)
reporter.add("Lorem ipsum")
reporter.add("Column1\tColumn2",heading=True)
reporter.add("1\t2")
reporter.add("3\t4")
reporter.add("Lorem more ipsum")
report_html = os.path.join(self.wd,"report.html")
reporter.write_html(report_html,
title="Test Document",
no_styles=True)
self.assertTrue(os.path.isfile(report_html))
expected_contents = """<html>
<head>
<title>Test Document</title>
</head>
<body>
<h1>Test Document</h1>
<div id='toc'>
<h2>Contents</h2>
<ul><li><a href='#This_is_a_Test'>This is a Test</a></li></ul>
</div>
<div id='This_is_a_Test'>
<h2>This is a Test</h2>
<p>Lorem ipsum</p>
</div>
<div>
<table>
<tr><th>Column1</th><th>Column2</th></tr>
<tr><td>1</td><td>2</td></tr>
<tr><td>3</td><td>4</td></tr>
</table>
</div>
<div>
<p>Lorem more ipsum</p>
</div></body>
</html>
"""
for expected,actual in zip(expected_contents.split('\n'),
open(report_html,'r').read().split('\n')):
self.assertEqual(expected,actual)
# Read counts from counts file(s)
counts = BarcodeCounter(*args)
elif len(args) == 1 and os.path.isdir(args[0]):
# Generate counts from bcl2fastq output
counts = count_barcodes_bcl2fastq(args[0])
else:
# Generate counts from fastq files
counts = count_barcodes(args)
# Deal with cutoff
if opts.cutoff == 0.0:
cutoff = None
else:
cutoff = opts.cutoff
# Report the counts
if not opts.no_report:
reporter = Reporter()
if lanes is None:
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,