def test_make_coverage_report_no_reference(self):
"""
Reference must exist
"""
gff = os.path.join(self._data_dir, 'alignment_summary.gff')
with self.assertRaises(IOError):
make_coverage_report(gff, 'foo', 'foo.json', 1, self._output_dir, '1', False)
def test_make_coverage_report_none_reference(self):
"""
Reference cannot be null
"""
gff = os.path.join(self._data_dir, 'alignment_summary.gff')
with self.assertRaises(PbReportError):
make_coverage_report(gff, None, 'foo.json', 1, self._output_dir, '1', False)
def test_make_coverage_report_no_gff(self):
"""
Gff exists
"""
with self.assertRaises(IOError):
make_coverage_report('foo', self.REFERENCE, 'foo.json', 1,
self._output_dir)
def test_make_coverage_report_none_reference(self):
"""
Reference cannot be null
"""
with self.assertRaises(PbReportError):
make_coverage_report(self.GFF, None, 'foo.json', 1,
self._output_dir)
def test_make_coverage_report_no_reference(self):
"""
Reference must exist
"""
with self.assertRaises(IOError):
make_coverage_report(self.GFF, 'foo', 'foo.json', 1,
self._output_dir)
def test_make_coverage_report_none_gff(self):
"""
Gff cannot be null
"""
with self.assertRaises(PbReportError):
make_coverage_report(None, self.REFERENCE, 'foo.json', 1,
self._output_dir)
def test_make_coverage_report_no_gff(self):
"""
Gff exists
"""
with self.assertRaises(IOError):
make_coverage_report('foo', self.REFERENCE, 'foo.json', 1,
self._output_dir)
def test_make_coverage_report_none_reference(self):
"""
Reference cannot be null
"""
with self.assertRaises(PbReportError):
make_coverage_report(
self.GFF, None, 'foo.json', 1, self._output_dir)
def test_make_coverage_report_no_reference(self):
"""
Reference must exist
"""
with self.assertRaises(IOError):
make_coverage_report(
self.GFF, 'foo', 'foo.json', 1, self._output_dir)
def test_make_coverage_report_none_gff(self):
"""
Gff cannot be null
"""
ref = os.path.join(self._data_dir, 'lambda')
with self.assertRaises(PbReportError):
make_coverage_report(None, ref, 'foo.json', 1, self._output_dir, '1', False)
def test_make_coverage_report_none_gff(self):
"""
Gff cannot be null
"""
with self.assertRaises(PbReportError):
make_coverage_report(None, self.REFERENCE, 'foo.json', 1,
self._output_dir)
def test_make_coverage_report_no_gff(self):
"""
Gff exists
"""
ref = os.path.join(self._data_dir, 'lambda')
with self.assertRaises(IOError):
make_coverage_report('foo', ref, 'foo.json', 1, self._output_dir, '1', False)
def test_make_report(self):
rpt = make_coverage_report(self.GFF, self.REFERENCE,
report=self.report_out,
output_dir=self.tmp_dir,
max_contigs_to_plot=25)
attr = {a.id:a.value for a in rpt.attributes}
self.assertEqual(attr['missing_bases_pct'], 0.0)
self.assertAlmostEqual(attr['depth_coverage_mean'], 68.06, places=2)
def test_make_report(self):
rpt = make_coverage_report(self.GFF,
self.REFERENCE,
report=self.report_out,
output_dir=self.tmp_dir,
max_contigs_to_plot=25)
attr = {a.id: a.value for a in rpt.attributes}
self.assertEqual(attr['missing_bases_pct'], 0.0)
self.assertEqual(int(attr['depth_coverage_mean']), 68)
def test_make_coverage_report(self):
"""
Create a report object, do assertions on its properties, then assert that it gets written
"""
report = make_coverage_report(self.GFF, self.REFERENCE, 25, 'rpt.json',
self._output_dir)
self.assertEqual(2, len(report.attributes))
self.assertEqual(0, len(report.tables))
self.assertEqual(2, len(report.plotGroups))
self.assertTrue(op.exists(op.join(self._output_dir, 'rpt.json')))
def test_make_coverage_report(self):
"""
Create a report object, do assertions on its properties, then assert that it gets written
"""
report = make_coverage_report(self.GFF, self.REFERENCE, 25, 'rpt.json',
self._output_dir)
self.assertEqual(2, len(report.attributes))
self.assertEqual(0, len(report.tables))
self.assertEqual(2, len(report.plotGroups))
self.assertTrue(op.exists(op.join(self._output_dir, 'rpt.json')))
validate_report_complete(self, report)
def test_plot_file_names(self):
report = make_coverage_report(self.GFF, self.REFERENCE, 25, 'rpt.json',
self._output_dir)
n = 0
for pg in report.plotGroups:
if pg.id == "coverage_plots":
for p in pg.plots:
if p.id.startswith("coverage_contig"):
self.assertEqual(self.PLOT_FILE_NAME,
op.basename(p.image))
n += 1
self.assertEqual(n, 1, "Contig coverage plot not found")
def test_plot_file_names(self):
report = make_coverage_report(self.GFF, self.REFERENCE, 25, 'rpt.json',
self._output_dir)
n = 0
for pg in report.plotGroups:
if pg.id == "coverage_plots":
for p in pg.plots:
if p.id.startswith("coverage_contig"):
self.assertEqual(self.PLOT_FILE_NAME,
op.basename(p.image))
n += 1
self.assertEqual(n, 1, "Contig coverage plot not found")
def test_make_coverage_report(self):
"""
Create a report object, do assertions on its properties, then assert that it gets written
"""
ref = os.path.join(self._data_dir, 'references', 'lambda')
gff = os.path.join(self._data_dir, 'alignment_summary.lambda.gff')
report = make_coverage_report(gff, ref, 25, 'rpt.json', self._output_dir, 60, False)
self.assertEqual(2, len(report.attributes))
self.assertEqual(0, len(report.tables))
self.assertEqual(2, len(report.plotGroups))
self.assertTrue(os.path.exists(os.path.join(self._output_dir, 'rpt.json')))
def _create_coverage_report(self):
"""
Creates and returns a coverage report
"""
from pbreports.report.coverage import make_coverage_report
datadir = os.path.join(ROOT_DATA_DIR, 'coverage')
log.info(
'Creating Coverage report using datadir {d}'.format(d=datadir))
ref = os.path.join(datadir, 'references', 'lambda')
gff = os.path.join(datadir, 'alignment_summary.lambda.gff')
max_contigs_to_plot = 25
dpi = 60
dumpdata = False
report_json = 'coverage.json'
output_json = os.path.join(self._output_dir, report_json)
make_coverage_report(gff, ref, max_contigs_to_plot, report_json,
self._output_dir, dpi, dumpdata)
return self._deserialize_report(output_json)
def _create_coverage_report(self):
"""
Creates and returns a coverage report
"""
from pbreports.report.coverage import make_coverage_report
datadir = os.path.join(ROOT_DATA_DIR, 'coverage')
log.info(
'Creating Coverage report using datadir {d}'.format(d=datadir))
ref = os.path.join(datadir, 'references', 'lambda')
gff = os.path.join(datadir, 'alignment_summary.lambda.gff')
max_contigs_to_plot = 25
dpi = 60
dumpdata = False
report_json = 'coverage.json'
output_json = os.path.join(self._output_dir, report_json)
make_coverage_report(gff, ref, max_contigs_to_plot,
report_json, self._output_dir, dpi, dumpdata)
return self._deserialize_report(output_json)
def run_report(args):
return make_coverage_report(args.gff, args.reference, args.maxContigs,
args.report, args.output, args.dpi, args.dumpdata)