def test_make_filter_stats_report_sts_xml(self):
"""
Test the content of the filter report generated from an sts.xml
"""
sts_xml = pbtestdata.get_file("stats-xml")
rpt = make_filter_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
self._compare_attribute_values(
report_d=d,
expected_d={
Constants.A_NBASES: 1672335649,
Constants.A_NREADS: 394658,
Constants.A_READ_N50: 7750,
Constants.A_READ_LENGTH: 4237,
},
)
self.assertTrue(os.path.exists(os.path.join(self.get_output_dir(), "readLenDist0.png")))
# self.assertTrue(os.path.exists(os.path.join(
# self.get_output_dir(),
# 'readQualDist0.png')))
# these are from a raw STS file
self.assertEqual(len(rpt._dataset_uuids), 0, "Incorrect report datasets uuids")
print pformat(rpt.to_dict())
validate_report_complete(self, rpt)
def test_make_filter_stats_report_sts_xml(self):
"""
Test the content of the filter report generated from an sts.xml
"""
sts_xml = pbtestdata.get_file("stats-xml")
rpt = make_filter_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
self._compare_attribute_values(report_d=d,
expected_d={
Constants.A_NBASES: 1672335649,
Constants.A_NREADS: 394658,
Constants.A_READ_N50: 7750,
Constants.A_READ_LENGTH: 4237
})
self.assertTrue(
os.path.exists(
os.path.join(self.get_output_dir(), 'readLenDist0.png')))
# self.assertTrue(os.path.exists(os.path.join(
# self.get_output_dir(),
# 'readQualDist0.png')))
# these are from a raw STS file
self.assertEqual(len(rpt._dataset_uuids), 0,
"Incorrect report datasets uuids")
print pformat(rpt.to_dict())
validate_report_complete(self, rpt)
def test_make_filter_stats_report_dataset(self):
"""
Test the content of the filter report generated from a dataset
"""
try:
log.info(
TestXMLstatsRpts.test_make_filter_stats_report_dataset.__doc__)
sts_xml = data.getXmlWithStats()
rpt = make_filter_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
self.assertEqual('Metrics', c0['header'])
self.assertEqual('filtering_stats_xml_report.filter_xml_table.'
'filter_names_column', c0['id'])
self.assertEqual('Polymerase Read Bases', c0['values'][0])
self.assertEqual('Polymerase Reads', c0['values'][1])
self.assertEqual('Polymerase Read N50', c0['values'][2])
self.assertEqual('Polymerase Read Length', c0['values'][3])
self.assertEqual('Polymerase Read Quality', c0['values'][4])
self.assertEqual('Values', c1['header'])
self.assertEqual('filtering_stats_xml_report.filter_xml_table.'
'filter_stats_column', c1['id'])
self.assertEqual(393167212.65, c1['values'][0])
self.assertEqual(25123, c1['values'][1])
self.assertEqual(21884, c1['values'][2])
self.assertEqual(15649.69, c1['values'][3])
self.assertEqual(0.86, c1['values'][4])
self.assertTrue(os.path.exists(os.path.join(
self.get_output_dir(),
'readLenDist0.png')))
self.assertTrue(os.path.exists(os.path.join(
self.get_output_dir(),
'readQualDist0.png')))
self.assertTrue(os.path.exists(os.path.join(
self.get_output_dir(),
'readLenDist1.png')))
self.assertTrue(os.path.exists(os.path.join(
self.get_output_dir(),
'readQualDist1.png')))
except:
log.error(traceback.format_exc())
raise
def test_make_filter_stats_report_dataset_multiple_chips(self):
sts_xml = data.getXmlWithStats()
rpt = make_filter_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
self._compare_attribute_values(
report_d=d,
expected_d={
Constants.A_NBASES: 342348413,
Constants.A_NREADS: 25123,
Constants.A_READ_N50: 21884,
Constants.A_READ_LENGTH: 13627,
},
)
self.assertTrue(os.path.exists(os.path.join(self.get_output_dir(), "readLenDist0.png")))
self.assertTrue(os.path.exists(os.path.join(self.get_output_dir(), "readLenDist1.png")))
def test_make_filter_stats_report_sts_xml(self):
"""
Test the content of the filter report generated from an sts.xml
"""
try:
log.info(
TestXMLstatsRpts.test_make_filter_stats_report_sts_xml.__doc__)
sts_xml = data.getStats(0)
rpt = make_filter_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
self.assertEqual('Metrics', c0['header'])
self.assertEqual('filtering_stats_xml_report.filter_xml_table.'
'filter_names_column', c0['id'])
self.assertEqual('Polymerase Read Bases', c0['values'][0])
self.assertEqual('Polymerase Reads', c0['values'][1])
self.assertEqual('Polymerase Read N50', c0['values'][2])
self.assertEqual('Polymerase Read Length', c0['values'][3])
self.assertEqual('Polymerase Read Quality', c0['values'][4])
self.assertEqual('Values', c1['header'])
self.assertEqual('filtering_stats_xml_report.filter_xml_table.'
'filter_stats_column', c1['id'])
self.assertEqual(4464266.29, c1['values'][0])
self.assertEqual(901, c1['values'][1])
self.assertEqual(6570, c1['values'][2])
self.assertEqual(4954.79, c1['values'][3])
self.assertEqual(0.83, c1['values'][4])
self.assertTrue(os.path.exists(os.path.join(
self.get_output_dir(),
'readLenDist0.png')))
self.assertTrue(os.path.exists(os.path.join(
self.get_output_dir(),
'readQualDist0.png')))
# these are from a raw STS file
self.assertEqual(len(rpt._dataset_uuids), 0,
"Incorrect report datasets uuids")
except:
log.error(traceback.format_exc())
raise
def test_make_filter_stats_report_dataset_multiple_chips(self):
sts_xml = data.getXmlWithStats()
rpt = make_filter_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
self._compare_attribute_values(report_d=d,
expected_d={
Constants.A_NBASES: 342348413,
Constants.A_NREADS: 25123,
Constants.A_READ_N50: 21884,
Constants.A_READ_LENGTH: 13627
})
self.assertTrue(
os.path.exists(
os.path.join(self.get_output_dir(), 'readLenDist0.png')))
self.assertTrue(
os.path.exists(
os.path.join(self.get_output_dir(), 'readLenDist1.png')))
def test_make_filter_stats_report_dataset(self):
"""
Test the content of the filter report generated from a dataset
"""
sts_xml = pbtestdata.get_file("subreads-sequel")
rpt = make_filter_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
self._compare_attribute_values(
report_d=d,
expected_d={
Constants.A_NBASES: 1672335649,
Constants.A_NREADS: 394658,
Constants.A_READ_N50: 7750,
Constants.A_READ_LENGTH: 4237,
},
)
self.assertTrue(os.path.exists(os.path.join(self.get_output_dir(), "readLenDist0.png")))
def test_make_filter_stats_report_dataset(self):
"""
Test the content of the filter report generated from a dataset
"""
sts_xml = pbtestdata.get_file("subreads-sequel")
rpt = make_filter_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
self._compare_attribute_values(report_d=d,
expected_d={
Constants.A_NBASES: 1672335649,
Constants.A_NREADS: 394658,
Constants.A_READ_N50: 7750,
Constants.A_READ_LENGTH: 4237
})
self.assertTrue(
os.path.exists(
os.path.join(self.get_output_dir(), 'readLenDist0.png')))
