def test_attributes_high_coverage(self):
tcs = get_top_contigs(self.REFERENCE, 25)
als = op.join(self._data_dir, "alignment_summary.lambda.gff")
pls = _get_contigs_to_plot(als, tcs)
contig = tcs[0]
c_cov = pls[contig.header]
stats = _get_reference_coverage_stats(pls.values())
att = _get_att_mean_coverage(stats)
# This was in coverage.xml for the alignment summary gff used
# attribute hidden="true" id="depth_coverage_mean" name="Coverage"
# value="2958.16">2958.16</attribute>
self.assertAlmostEqual(2958.16, att.value, places=2)
att = _get_att_percent_missing(stats)
self.assertEqual(0, att.value)
def test_attributes_high_coverage(self):
tcs = get_top_contigs(self.REFERENCE, 25)
als = op.join(self._data_dir, "alignment_summary.lambda.gff")
pls = _get_contigs_to_plot(als, tcs)
contig = tcs[0]
c_cov = pls[contig.header]
stats = _get_reference_coverage_stats(pls.values())
att = _get_att_mean_coverage(stats)
# This was in coverage.xml for the alignment summary gff used
# attribute hidden="true" id="depth_coverage_mean" name="Coverage"
# value="2958.16">2958.16</attribute>
self.assertEqual(2958, int(att.value))
att = _get_att_percent_missing(stats)
self.assertEqual(0, att.value)
def test_attributes(self):
"""
Test that attribute values match expected
"""
tcs = get_top_contigs(self.REFERENCE, 25)
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
contig = tcs[0]
c_cov = pls[contig.header]
stats = _get_reference_coverage_stats(pls.values())
att = _get_att_mean_coverage(stats)
# This was in coverage.xml for the alignment summary gff used
# attribute hidden="true" id="depth_coverage_mean" name="Coverage"
# value="2958.16">2958.16</attribute>
self.assertAlmostEqual(1.228, att.value, places=3)
att = _get_att_percent_missing(stats)
self.assertAlmostEqual(58.4, att.value, places=1)
def test_attributes(self):
"""
Test that attribute values match expected
"""
tcs = get_top_contigs(self.REFERENCE, 25)
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
contig = tcs[0]
c_cov = pls[contig.header]
stats = _get_reference_coverage_stats(pls.values())
att = _get_att_mean_coverage(stats)
# This was in coverage.xml for the alignment summary gff used
# attribute hidden="true" id="depth_coverage_mean" name="Coverage"
# value="2958.16">2958.16</attribute>
self.assertEqual(1, int(att.value))
att = _get_att_percent_missing(stats)
self.assertAlmostEqual(0.584, att.value, places=3)
def test_attributes(self):
"""
Test that attribute values match expected
"""
ref = os.path.join(self._data_dir, 'references', 'lambda')
tcs = get_top_contigs(ref, 25)
als = os.path.join(self._data_dir, 'alignment_summary.lambda.gff')
pls = _get_contigs_to_plot(als, tcs)
contig = tcs[0]
c_cov = pls[contig.header]
stats = _get_reference_coverage_stats(pls.values())
att = _get_att_mean_coverage(stats)
# This was in coverage.xml for the alignment summary gff used
# attribute hidden="true" id="depth_coverage_mean" name="Coverage" value="2958.16">2958.16</attribute>
self.assertEqual(2958.1640346377467, att.value)
att = _get_att_percent_missing(stats)
self.assertEqual(0, att.value)
