def test_get_consensus_table(self):
"""
Test the data in the table object and the attributes
"""
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
table, attributes = _get_consensus_table_and_attributes(ref_data, self._get_reference_entry())
self.assertEqual(5, len(table.columns))
self.assertEqual(self.CONTIG_ID, table.columns[0].values[0])
self.assertEqual(self.TEST_VALUES["contig_len"],
table.columns[1].values[0])
self.assertEqual(1, table.columns[2].values[0])
self.assertAlmostEqual(self.TEST_VALUES["concordance"],
table.columns[3].values[0], places=4)
self.assertAlmostEqual(self.TEST_VALUES["coverage"],
table.columns[4].values[0], places=2)
def test_get_consensus_table(self):
"""
Test the data in the table object and the attributes
"""
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY,
top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
table, attributes = _get_consensus_table_and_attributes(
ref_data, self._get_reference_entry())
self.assertEqual(5, len(table.columns))
self.assertEqual(self.CONTIG_ID, table.columns[0].values[0])
self.assertEqual(self.TEST_VALUES["contig_len"],
table.columns[1].values[0])
self.assertEqual(1, table.columns[2].values[0])
self.assertAlmostEqual(self.TEST_VALUES["concordance"],
table.columns[3].values[0],
places=4)
self.assertAlmostEqual(self.TEST_VALUES["coverage"],
table.columns[4].values[0],
places=2)
def test_get_consensus_attributes(self):
"""
Test the data in the table object and the attributes
"""
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
table, attributes = _get_consensus_table_and_attributes(ref_data, self._get_reference_entry())
self.assertEqual(5, len(attributes))
def __get_att_val(_id, atts):
for a in atts:
if a.id == _id:
return a.value
self.assertEqual(self.TEST_VALUES["contig_len"], __get_att_val("mean_contig_length", attributes))
self.assertAlmostEqual(
self.TEST_VALUES["bases_called"], __get_att_val("weighted_mean_bases_called", attributes), places=4
)
self.assertAlmostEqual(
self.TEST_VALUES["concordance"], __get_att_val("weighted_mean_concordance", attributes), places=4
)
self.assertAlmostEqual(
self.TEST_VALUES["coverage"], __get_att_val("weighted_mean_coverage", attributes), places=2
)
self.assertEqual(self.CONTIG_ID, __get_att_val("longest_contig_name", attributes))
def test_append_variants_gff_data(self):
"""
Test that ERR information gets added to the ref_data dict
"""
# top_contigs = get_top_contigs(ref, 2)
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(self.TEST_VALUES["n_gff_err_1"], results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(self.TEST_VALUES["n_gff_err_2"], results[ERR])
def test_get_consensus_attributes(self):
"""
Test the data in the table object and the attributes
"""
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY,
top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
table, attributes = _get_consensus_table_and_attributes(
ref_data, self._get_reference_entry())
self.assertEqual(5, len(attributes))
def __get_att_val(_id, atts):
for a in atts:
if a.id == _id:
return a.value
self.assertEqual(self.TEST_VALUES["contig_len"],
__get_att_val('mean_contig_length', attributes))
self.assertAlmostEqual(self.TEST_VALUES["bases_called"],
__get_att_val('weighted_mean_bases_called',
attributes),
places=4)
self.assertAlmostEqual(self.TEST_VALUES["concordance"],
__get_att_val('weighted_mean_concordance',
attributes),
places=4)
self.assertAlmostEqual(self.TEST_VALUES["coverage"],
__get_att_val('weighted_mean_coverage',
attributes),
places=2)
self.assertEqual(self.CONTIG_ID,
__get_att_val('longest_contig_name', attributes))
def test_append_variants_gff_data(self):
"""
Test that ERR information gets added to the ref_data dict
"""
# top_contigs = get_top_contigs(ref, 2)
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY,
top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(self.TEST_VALUES["n_gff_err_1"], results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(self.TEST_VALUES["n_gff_err_2"], results[ERR])
