def test_top_contigs(self):
"""
Test top contigs from ref
"""
ref = op.join(LOCAL_DATA, "coverage", 'simple3', "sequence",
"simple3.fasta")
self.assertEqual(2, len(get_top_contigs(ref, 2)))
def test_top_contigs(self):
"""
Test top contigs from ref
"""
ref = op.join(LOCAL_DATA, "coverage", 'simple3', "sequence",
"simple3.fasta")
self.assertEqual(2, len(get_top_contigs(ref, 2)))
def test_get_coverage_stats(self):
"""
Test the coverage stats object (needs more)
"""
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())
self.assertEqual(485, len(stats.means))
def test_create_histogram(self):
"""
Simple (non null) test of histogram
"""
tcs = get_top_contigs(self.REFERENCE, 25)
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
stats = _get_reference_coverage_stats(pls.values())
fig, ax = _create_histogram(stats)
self.assertIsNotNone(fig)
self.assertIsNotNone(ax)
def test_create_histogram(self):
"""
Simple (non null) test of histogram
"""
tcs = get_top_contigs(self.REFERENCE, 25)
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
stats = _get_reference_coverage_stats(pls.values())
fig, ax = CoverageReport()._create_histogram(stats)
self.assertIsNotNone(fig)
self.assertIsNotNone(ax)
def test_get_coverage_stats(self):
"""
Test the coverage stats object (needs more)
"""
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())
self.assertEqual(485, len(stats.means))
def test_create_contig_plot(self):
"""
Simple non-null test of single contig fig,ax
"""
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]
fig, ax = _create_contig_plot(c_cov)
self.assertIsNotNone(fig)
self.assertIsNotNone(ax)
def test_get_coverage_stats(self):
"""
Test the coverage stats object (needs more)
"""
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())
self.assertEqual(485, len(stats.means))
def test_create_contig_plot(self):
"""
Simple non-null test of single contig fig,ax
"""
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]
fig, ax = CoverageReport()._create_contig_plot(c_cov)
self.assertIsNotNone(fig)
self.assertIsNotNone(ax)
def test_contigs_to_plot(self):
"""
Test top contigs from ref
"""
tcs = get_top_contigs(self.REFERENCE, 25)
self.assertEqual(1, len(tcs))
# op.join(self._data_dir, 'alignment_summary.lambda.gff')
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
self.assertEqual(len(pls), len(tcs))
contig = tcs[0]
c_cov = pls[contig.header]
self.assertEqual(self.CONTIG_ID, c_cov._name)
self.assertEqual(self.PLOT_FILE_NAME, op.basename(c_cov.file_name))
def test_contigs_to_plot(self):
"""
Test top contigs from ref
"""
ref = os.path.join(self._data_dir, 'references', 'lambda')
tcs = get_top_contigs(ref, 25)
self.assertEqual(1, len(tcs))
als = os.path.join(self._data_dir, 'alignment_summary.lambda.gff')
pls = _get_contigs_to_plot(als, tcs)
self.assertEqual(len(pls), len(tcs))
contig = tcs[0]
c_cov = pls[contig.header]
self.assertEqual('lambda_NEB3011', c_cov._name)
def test_create_contig_plot(self):
"""
Simple non-null test of single contig fig,ax
"""
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]
fig, ax = _create_contig_plot(c_cov)
self.assertIsNotNone(fig)
self.assertIsNotNone(ax)
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_contigs_to_plot(self):
"""
Test top contigs from ref
"""
tcs = get_top_contigs(self.REFERENCE, 25)
self.assertEqual(1, len(tcs))
# op.join(self._data_dir, 'alignment_summary.lambda.gff')
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
self.assertEqual(len(pls), len(tcs))
contig = tcs[0]
c_cov = pls[contig.header]
self.assertEqual(self.CONTIG_ID, c_cov._name)
self.assertEqual(self.PLOT_FILE_NAME, op.basename(c_cov.file_name))
def test_create_coverage_histo_plot_grp(self):
"""
Test that plotGroup of the histogram is created as expected
"""
tcs = get_top_contigs(self.REFERENCE, 25)
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
stats = _get_reference_coverage_stats(pls.values())
plot_group = _create_coverage_histo_plot_grp(stats, self._output_dir)
# only 1 histo
self.assertEqual(1, len(plot_group.plots))
self._assert_image_file(plot_group.thumbnail)
for plot in plot_group.plots:
self._assert_image_file(plot.image)
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_create_histogram(self):
"""
Simple (non null) test of histogram
"""
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)
stats = _get_reference_coverage_stats(pls.values())
fig, ax = _create_histogram(stats)
self.assertIsNotNone(fig)
self.assertIsNotNone(ax)
def test_create_coverage_plot_grp(self):
"""
Test that plotGroup of coverage plots is created as expected
"""
tcs = get_top_contigs(self.REFERENCE, 25)
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
plot_group = _create_coverage_plot_grp(tcs, pls, self._output_dir)
# only 1 contig in lambda
self.assertEqual(1, len(plot_group.plots))
self._assert_image_file(plot_group.thumbnail)
for plot in plot_group.plots:
self._assert_image_file(plot.image)
def test_create_coverage_plot_grp(self):
"""
Test that plotGroup of coverage plots is created as expected
"""
tcs = get_top_contigs(self.REFERENCE, 25)
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
plot_group = CoverageReport()._create_coverage_plot_grp(
tcs, pls, self._output_dir)
# only 1 contig in lambda
self.assertEqual(1, len(plot_group.plots))
self._assert_image_file(plot_group.thumbnail)
for plot in plot_group.plots:
self._assert_image_file(plot.image)
def test_create_coverage_histo_plot_grp(self):
"""
Test that plotGroup of the histogram is created as expected
"""
tcs = get_top_contigs(self.REFERENCE, 25)
als = self.GFF
pls = _get_contigs_to_plot(als, tcs)
stats = _get_reference_coverage_stats(pls.values())
plot_group = CoverageReport()._create_coverage_histo_plot_grp(
stats, self._output_dir)
# only 1 histo
self.assertEqual(1, len(plot_group.plots))
self._assert_image_file(plot_group.thumbnail)
for plot in plot_group.plots:
self._assert_image_file(plot.image)
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_create_coverage_plot_grp(self):
"""
Test that plotGroup of coverage plots is created as 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)
plot_group = _create_coverage_plot_grp(tcs, pls, self._output_dir)
# only 1 contig in lambda
self.assertEqual(1, len(plot_group.plots))
self._assert_image_file(plot_group.thumbnail)
for plot in plot_group.plots:
self._assert_image_file(plot.image)
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 make_report(self, gff, reference, max_contigs_to_plot, report,
output_dir):
"""
Entry to report.
:param gff: (str) path to alignment_summary.gff
:param reference: (str) path to reference_dir
:param max_contigs_to_plot: (int) max number of contigs to plot
"""
_validate_inputs(gff, reference)
top_contigs = get_top_contigs(reference, max_contigs_to_plot)
cov_map = _get_contigs_to_plot(gff, top_contigs)
# stats may be None
stats = _get_reference_coverage_stats(cov_map.values())
a1 = _get_att_mean_coverage(stats)
a2 = _get_att_percent_missing(stats)
plot_grp_coverage = self._create_coverage_plot_grp(
top_contigs, cov_map, output_dir)
plot_grp_histogram = None
if stats is not None:
plot_grp_histogram = self._create_coverage_histo_plot_grp(
stats, output_dir)
plotgroups = []
# Don't add the Plot Group if no plots are added
if plot_grp_coverage.plots:
plotgroups.append(plot_grp_coverage)
if plot_grp_histogram is not None:
# Don't add the Plot Group if no plots are added
if plot_grp_histogram.plots:
plotgroups.append(plot_grp_histogram)
rpt = Report(self.spec.id,
plotgroups=plotgroups,
attributes=[a1, a2],
dataset_uuids=(ReferenceSet(reference).uuid,))
rpt = self.spec.apply_view(rpt)
rpt.write_json(os.path.join(output_dir, report))
return rpt
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)
def make_coverage_report(gff, reference, max_contigs_to_plot, report,
output_dir):
"""
Entry to report.
:param gff: (str) path to alignment_summary.gff
:param reference: (str) path to reference_dir
:param max_contigs_to_plot: (int) max number of contigs to plot
"""
_validate_inputs(gff, reference)
top_contigs = get_top_contigs(reference, max_contigs_to_plot)
cov_map = _get_contigs_to_plot(gff, top_contigs)
# stats may be None
stats = _get_reference_coverage_stats(cov_map.values())
a1 = _get_att_mean_coverage(stats)
a2 = _get_att_percent_missing(stats)
plot_grp_coverage = _create_coverage_plot_grp(
top_contigs, cov_map, output_dir)
plot_grp_histogram = None
if stats is not None:
plot_grp_histogram = _create_coverage_histo_plot_grp(stats, output_dir)
plotgroups = []
# Don't add the Plot Group if no plots are added
if plot_grp_coverage.plots:
plotgroups.append(plot_grp_coverage)
if plot_grp_histogram is not None:
# Don't add the Plot Group if no plots are added
if plot_grp_histogram.plots:
plotgroups.append(plot_grp_histogram)
rpt = Report('coverage',
title="Coverage",
plotgroups=plotgroups,
attributes=[a1, a2],
dataset_uuids=(ReferenceSet(reference).uuid,))
rpt.write_json(os.path.join(output_dir, report))
return rpt
def test_get_top_contigs(self):
top_contigs = get_top_contigs(self.REFERENCE, 25)
self.assertTrue(len(top_contigs), 25)
def test__get_contigs_to_plot(self):
top_contigs = get_top_contigs(self.REFERENCE, 25)
cov_map = _get_contigs_to_plot(self.GFF, top_contigs)
self.assertNotEqual(len(cov_map), 0)
def test_top_contigs(self):
"""
Test top contigs from ref
"""
ref = os.path.join(self._data_dir, 'references', 'simple3')
self.assertEqual(2, len(get_top_contigs(ref, 2)))
def test_get_top_contigs(self):
top_contigs = get_top_contigs(self.REFERENCE, 25)
self.assertTrue(len(top_contigs), 25)
def test__get_contigs_to_plot(self):
top_contigs = get_top_contigs(self.REFERENCE, 25)
cov_map = _get_contigs_to_plot(self.GFF, top_contigs)
self.assertNotEqual(len(cov_map), 0)
