def testMulticoreAnnotate(self):
"""Test a (too) simple annotating exercise from GAF on 2 cores"""
gafDatasource = TestUtils.createGafDatasourceProxy(self.config)
# Test pickling
dump(gafDatasource, file('out/testGAFPickle.pkl','w'))
m1 = MutationData()
m1.chr = '3'
m1.start = '178866811'
m1.end = '178866811'
m1.ref_allele = "A"
m1.alt_allele = "C"
m1.build = "hg19"
m2 = MutationData()
m2.chr = '3'
m2.start = '178866812'
m2.end = '178866812'
m2.ref_allele = "A"
m2.alt_allele = "C"
m2.build = "hg19"
p = LoggingPool(processes=2)
result = p.map(annotate_mutation_global, [(gafDatasource, m1), (gafDatasource, m2)])
p.close()
p.join()
for r in result:
self.assertTrue("transcript_id" in r.keys())
self.assertTrue("gene" in r.keys())
self.assertTrue(r["gene"] == "PIK3CA")
self.assertTrue(result[0].start != result[1].start)
def testMulticoreAnnotate(self):
"""Test a (too) simple annotating exercise from GAF on 2 cores"""
gafDatasource = TestUtils.createGafDatasourceProxy(self.config)
# Test pickling
dump(gafDatasource, file('out/testGAFPickle.pkl', 'w'))
m1 = MutationData()
m1.chr = '3'
m1.start = '178866811'
m1.end = '178866811'
m1.ref_allele = "A"
m1.alt_allele = "C"
m1.build = "hg19"
m2 = MutationData()
m2.chr = '3'
m2.start = '178866812'
m2.end = '178866812'
m2.ref_allele = "A"
m2.alt_allele = "C"
m2.build = "hg19"
p = LoggingPool(processes=2)
result = p.map(annotate_mutation_global, [(gafDatasource, m1),
(gafDatasource, m2)])
p.close()
p.join()
for r in result:
self.assertTrue("transcript_id" in r.keys())
self.assertTrue("gene" in r.keys())
self.assertTrue(r["gene"] == "PIK3CA")
self.assertTrue(result[0].start != result[1].start)
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_v19_ds("out/test_hgvs_annotations_SNP_")
# 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_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_v19_ds("out/test_hgvs_annotations_no_mapping_file_", 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_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')
