def test_overlapping_gene_5flank(self):
"""Test that we can collect an overlapping gene on its 5' Flank """
ds = TestUtils._create_test_gencode_ds("out/overlapping_genes_flank")
txs = ds.get_overlapping_transcripts("22", 22222050, 22222050, padding=100)
self.assertTrue( len(txs) == 1)
self.assertTrue(txs[0].get_transcript_id() == "ENST00000398822.3")
txs = ds.get_overlapping_transcripts("22", 22224920, 22224920)
self.assertTrue(len(txs) == 0)
def test_hgvs_annotations_IGR(self):
"""Test that the HGVS annotations appear for IGR"""
ds = TestUtils._create_test_gencode_ds("out/test_hgvs_annotations_IGR_")
m = MutationData()
m.createAnnotation('variant_type', 'SNP')
m.createAnnotation('build', 'hg19')
m.createAnnotation('variant_classification', 'IGR')
m.createAnnotation('chr', '15')
m.createAnnotation('start', 30938316)
m.createAnnotation('end', 30938316)
m.createAnnotation('ref_allele', 'G')
m.createAnnotation('alt_allele', 'A')
m2 = ds.annotate_mutation(m)
self.assertEqual(m2.get('HGVS_genomic_change', None), 'chr15.hg19:g.30938316G>A')
self.assertEqual(m2.get('HGVS_coding_DNA_change', None), '')
self.assertEqual(m2.get('HGVS_protein_change', None), '')
def test_hgvs_annotations_simple_SNP(self):
"""Test that HGVS annotations appear (incl. protein change) in a mutation, so we believe that the Transcript objects are populated properly."""
ds = TestUtils._create_test_gencode_ds("out/test_hgvs_annotations_")
# Now for a negative strand
m = MutationData()
m.chr = "22"
m.start = "22221730"
m.end = "22221730"
m.ref_allele = "T"
m.alt_allele = "G"
m.build = "hg19"
m2 = ds.annotate_mutation(m)
self.assertEqual(m2.get('HGVS_genomic_change', None), 'chr22.hg19:g.22221730T>G')
self.assertEqual(m2.get('HGVS_coding_DNA_change', None), 'ENST00000215832.6:c.1A>C')
self.assertEqual(m2.get('HGVS_protein_change', None), 'ENSP00000215832:p.Met1Leu')
def test_no_mapping_file(self):
"""Test that we can still create (from scratch) and instantiate a EnsemblDatasource when no protein mapping is specified (i.e. limited HGVS support)"""
"""Test that HGVS annotations appear (incl. protein change) in a mutation, so we believe that the Transcript objects are populated properly."""
ds = TestUtils._create_test_gencode_ds("out/test_hgvs_annotations_no_mapping_", protein_id_mapping_file=None)
# Now for a negative strand
m = MutationData()
m.chr = "22"
m.start = "22221730"
m.end = "22221730"
m.ref_allele = "T"
m.alt_allele = "G"
m.build = "hg19"
m2 = ds.annotate_mutation(m)
self.assertEqual(m2.get('HGVS_genomic_change', None), 'chr22.hg19:g.22221730T>G')
self.assertEqual(m2.get('HGVS_coding_DNA_change', None), 'ENST00000215832.6:c.1A>C')
self.assertEqual(m2.get('HGVS_protein_change', None), 'unknown_prot_seq_id:p.Met1Leu')
def test_small_positive_strand_transcript_change(self):
"""Test one location on a transcript and make sure that the transcript change rendered properly """
ds = TestUtils._create_test_gencode_ds("out/small_positive_strand_")
# Now for a negative strand
m = MutationData()
m.chr = "22"
m.start = "22221730"
m.end = "22221730"
m.ref_allele = "T"
m.alt_allele = "G"
m2 = ds.annotate_mutation(m)
self.assertTrue(m2['transcript_change'] == "c.1A>C", "Incorrect transcript change: " + m2['transcript_change'])
# positive strand
m = MutationData()
m.chr = "3"
m.start = "178916614"
m.end = "178916614"
m.ref_allele = "G"
m.alt_allele = "T"
m2 = ds.annotate_mutation(m)
self.assertTrue(m2['transcript_change'] == "c.1G>T", "Incorrect transcript change: " + m2['transcript_change'])
def test_overlapping_gene(self):
"""Test that we can collect an overlapping gene """
ds = TestUtils._create_test_gencode_ds("out/overlapping_genes_")
genes = ds.get_overlapping_genes("22", 22115000, 22120000)
self.assertTrue(len(set(["MAPK1"]) - genes) == 0)
def test_overlapping_multiple_genes(self):
"""Test that we can collect multiple overlapping genes """
ds = TestUtils._create_test_gencode_ds("out/overlapping_genes_multiple_")
genes = ds.get_overlapping_genes("22", 22080000, 22120000)
self.assertTrue(len(set(["MAPK1", "YPEL1"]) - genes) ==0 )
