def test_minor_variant_table_builder(self):
"""
Test the length and values of a table produced by the minor variant table builder
"""
tb = MinorVariantTableBuilder()
self.assertEqual('top_minor_variants_table', tb.table.id)
columns = tb.table.columns
self.assertEqual(7, len(columns))
ref = self.REFERENCE
gff = self.RARE_VARIANTS_GFF
vf = VariantFinder(gff, ref, 100, 10000)
v = vf.find_top()[0]
tb.add_variant(v)
columns = tb.table.columns
self.assertEqual(self.CONTIG_ID, columns[0].values[0])
self.assertEqual(35782L, columns[1].values[0])
self.assertEqual('35782G>T', columns[2].values[0])
self.assertEqual('SUB', columns[3].values[0])
self.assertEqual(742, columns[4].values[0])
self.assertEqual(7, columns[5].values[0])
self.assertEqual(9, columns[6].values[0])
def test_variant_table_builder(self):
"""
Test the length and values of a table produced by the standard variant table builder
"""
tb = VariantTableBuilder()
columns = tb.table.columns
self.assertEqual('top_variants_table', tb.table.id)
self.assertEqual(7, len(columns))
ref = self.REFERENCE
gff = self.VARIANTS_GFF
vf = VariantFinder(gff, ref, 100, 10000)
top = vf.find_top()
for v in top:
tb.add_variant(v)
columns = tb.table.columns
# This tests the first row
for i in range(7):
self.assertEqual(self.TABLE_ROW_FIRST[i], columns[i].values[0])
for i in range(7):
self.assertEqual(self.TABLE_ROW_LAST[i], columns[i].values[-1])
def test_variant_table_builder(self):
"""
Test the length and values of a table produced by the standard variant table builder
"""
tb = VariantTableBuilder()
columns = tb.table.columns
self.assertEqual('top_variants_table', tb.table.id)
self.assertEqual(7, len(columns))
ref = self.REFERENCE
gff = self.VARIANTS_GFF
vf = VariantFinder(gff, ref, 100, 10000)
top = vf.find_top()
for v in top:
tb.add_variant(v)
columns = tb.table.columns
# This tests the first row
for i in range(7):
self.assertEqual(self.TABLE_ROW_FIRST[i], columns[i].values[0])
for i in range(7):
self.assertEqual(self.TABLE_ROW_LAST[i], columns[i].values[-1])
def test_variant_table_builder(self):
"""
Test the length and values of a table produced by the standard variant table builder
"""
tb = VariantTableBuilder()
columns = tb.table.columns
self.assertEqual('top_variants_table', tb.table.id)
self.assertEqual(7, len(columns))
self.assertEqual('Sequence', columns[0].header)
self.assertEqual('Position', columns[1].header)
self.assertEqual('Variant', columns[2].header)
self.assertEqual('Type', columns[3].header)
self.assertEqual('Coverage', columns[4].header)
self.assertEqual('Confidence', columns[5].header)
self.assertEqual('Genotype', columns[6].header)
ref = self.REFERENCE
gff = self.VARIANTS_GFF
vf = VariantFinder(gff, ref, 100, 10000)
top = vf.find_top()
for v in top:
tb.add_variant(v)
columns = tb.table.columns
# This tests the first row
for i in range(7):
self.assertEqual(self.TABLE_ROW_FIRST[i], columns[i].values[0])
for i in range(7):
self.assertEqual(self.TABLE_ROW_LAST[i], columns[i].values[-1])
def test_minor_variant_table_builder(self):
"""
Test the length and values of a table produced by the minor variant table builder
"""
tb = MinorVariantTableBuilder()
self.assertEqual('top_minor_variants_table', tb.table.id)
columns = tb.table.columns
self.assertEqual(7, len(columns))
ref = self.REFERENCE
gff = self.RARE_VARIANTS_GFF
vf = VariantFinder(gff, ref, 100, 10000)
v = vf.find_top()[0]
tb.add_variant(v)
columns = tb.table.columns
self.assertEqual(self.CONTIG_ID, columns[0].values[0])
self.assertEqual(35782L, columns[1].values[0])
self.assertEqual('35782G>T', columns[2].values[0])
self.assertEqual('SUB', columns[3].values[0])
self.assertEqual(742, columns[4].values[0])
self.assertEqual(7, columns[5].values[0])
self.assertEqual(9, columns[6].values[0])
def test_variant_finder(self):
ref = self.REFERENCE
gff = self.VARIANTS_GFF
vf = VariantFinder(gff, ref, 100, 10000)
top = vf.find_top()
self.assertEqual(self.N_TOP_VARIANTS, len(top))
def test_variant_finder(self):
ref = self.REFERENCE
gff = self.VARIANTS_GFF
vf = VariantFinder(gff, ref, 100, 10000)
top = vf.find_top()
self.assertEqual(self.N_TOP_VARIANTS, len(top))