def test_contigs_to_genes_one_hit(self):
"""Tests that given one blast hit, will give the correct keys and values"""
gene_detector = GeneDetector('madansi/tests/data/assembly.fa',
'madansi/tests/data/one_blast_hit')
self.assertCountEqual(list(gene_detector.contigs_to_genes().keys()),
['Contig1', 'Contig2', 'Contig3'])
self.assertEqual(
gene_detector.contigs_to_genes()['Contig2'].gene_objects, {})
self.assertEqual(
gene_detector.contigs_to_genes()['Contig3'].gene_objects, {})
self.assertCountEqual(
list(gene_detector.contigs_to_genes()
['Contig1'].gene_objects.keys()), ['gene1'])
my_gene = Gene(-1, 402, 1, None, 'Contig1', 3)
self.assertEqual(
gene_detector.contigs_to_genes()
['Contig1'].gene_objects['gene1'].orientation, my_gene.orientation)
self.assertEqual(
gene_detector.contigs_to_genes()
['Contig1'].gene_objects['gene1'].start, my_gene.start)
self.assertEqual(
gene_detector.contigs_to_genes()
['Contig1'].gene_objects['gene1'].end, my_gene.end)
self.assertEqual(
gene_detector.contigs_to_genes()
['Contig1'].gene_objects['gene1'].node, my_gene.node)
self.assertEqual(
gene_detector.contigs_to_genes()
['Contig1'].gene_objects['gene1'].contig, my_gene.contig)
self.assertEqual(
gene_detector.contigs_to_genes()
['Contig1'].gene_objects['gene1'].qry_start, my_gene.qry_start)
def test_contigs_to_genes_four_hits(self):
"""Tests output for multiple blast hits"""
gene_detector = GeneDetector('madansi/tests/data/assembly.fa', 'madansi/tests/data/four_blast_hits' )
self.assertCountEqual(list(gene_detector.contigs_to_genes().keys()), ['Contig1', 'Contig2', 'Contig3'])
self.assertCountEqual(list(gene_detector.contigs_to_genes()['Contig1'].gene_objects.keys()), ['gene1', 'gene2', 'gene3'])
self.assertCountEqual(list(gene_detector.contigs_to_genes()['Contig2'].gene_objects.keys()), ['geneA'])
self.assertCountEqual(list(gene_detector.contigs_to_genes()['Contig3'].gene_objects.keys()), [])
def test_contigs_to_genes_no_hits(self):
"""Tests that the correct keys are given in the contigs object and that there is no value for each contig in this object"""
gene_detector = GeneDetector('madansi/tests/data/assembly.fa',
'madansi/tests/data/empty_file')
self.assertCountEqual(list(gene_detector.contigs_to_genes().keys()),
['Contig1', 'Contig2', 'Contig3'])
self.assertEqual(
gene_detector.contigs_to_genes()['Contig1'].gene_objects, {})
def test_contigs_to_genes_four_hits(self):
"""Tests output for multiple blast hits"""
gene_detector = GeneDetector('madansi/tests/data/assembly.fa',
'madansi/tests/data/four_blast_hits')
self.assertCountEqual(list(gene_detector.contigs_to_genes().keys()),
['Contig1', 'Contig2', 'Contig3'])
self.assertCountEqual(
list(gene_detector.contigs_to_genes()
['Contig1'].gene_objects.keys()), ['gene1', 'gene2', 'gene3'])
self.assertCountEqual(
list(gene_detector.contigs_to_genes()
['Contig2'].gene_objects.keys()), ['geneA'])
self.assertCountEqual(
list(gene_detector.contigs_to_genes()
['Contig3'].gene_objects.keys()), [])
def test_contigs_to_genes_one_hit(self):
"""Tests that given one blast hit, will give the correct keys and values"""
gene_detector = GeneDetector('madansi/tests/data/assembly.fa', 'madansi/tests/data/one_blast_hit')
self.assertCountEqual(list(gene_detector.contigs_to_genes().keys()), ['Contig1', 'Contig2', 'Contig3'])
self.assertEqual(gene_detector.contigs_to_genes()['Contig2'].gene_objects, {})
self.assertEqual(gene_detector.contigs_to_genes()['Contig3'].gene_objects, {})
self.assertCountEqual(list(gene_detector.contigs_to_genes()['Contig1'].gene_objects.keys()), ['gene1'])
my_gene = Gene(-1,402,1,None, 'Contig1',3)
self.assertEqual(gene_detector.contigs_to_genes()['Contig1'].gene_objects['gene1'].orientation, my_gene.orientation)
self.assertEqual(gene_detector.contigs_to_genes()['Contig1'].gene_objects['gene1'].start, my_gene.start)
self.assertEqual(gene_detector.contigs_to_genes()['Contig1'].gene_objects['gene1'].end, my_gene.end)
self.assertEqual(gene_detector.contigs_to_genes()['Contig1'].gene_objects['gene1'].node, my_gene.node)
self.assertEqual(gene_detector.contigs_to_genes()['Contig1'].gene_objects['gene1'].contig, my_gene.contig)
self.assertEqual(gene_detector.contigs_to_genes()['Contig1'].gene_objects['gene1'].qry_start, my_gene.qry_start)
def test_contigs_to_genes_no_hits(self):
"""Tests that the correct keys are given in the contigs object and that there is no value for each contig in this object"""
gene_detector = GeneDetector('madansi/tests/data/assembly.fa', 'madansi/tests/data/empty_file')
self.assertCountEqual(list(gene_detector.contigs_to_genes().keys()), ['Contig1', 'Contig2', 'Contig3'])
self.assertEqual(gene_detector.contigs_to_genes()['Contig1'].gene_objects, {})