def test_appris_selects_transcript(self):
m = MutationData(chr="2", start="201722365", end="201722366", ref_allele="AC", alt_allele="-", build="hg19")
transcript_ds = TestUtils.createTranscriptProviderDatasource(self.config)
m = transcript_ds.annotate_mutation(m)
tx = transcript_ds.get_transcript(m['annotation_transcript'])
self.assertTrue(tx is not None, "Transcript was None when it should have been found. Does the ground truth transcript above need to be updated?")
self.assertEqual(tx._transcript_id,'ENST00000321356.4')
def test_appris_selects_transcript(self):
m = MutationDataFactory.default_create(chr="2", start="201722365", end="201722366", ref_allele="AC", alt_allele="-", build="hg19")
transcript_ds = TestUtils.createTranscriptProviderDatasource(self.config)
m = transcript_ds.annotate_mutation(m)
tx = transcript_ds.get_transcript(m['annotation_transcript'])
self.assertTrue(tx is not None, "Transcript was None when it should have been found. Does the ground truth transcript above need to be updated?")
self.assertEqual(tx._transcript_id,'ENST00000321356.4')
def _get_chosen_tx_and_transcript_ds(self, chrom, loc):
config = TestUtils.createUnitTestConfig()
transcript_ds = TestUtils.createTranscriptProviderDatasource(config)
transcript_ds.set_tx_mode(TranscriptProvider.TX_MODE_CANONICAL)
start_txs = transcript_ds.get_transcripts_by_pos(chr=chrom, start=str(loc), end=str(loc))
chosen_tx = transcript_ds._choose_transcript(start_txs, transcript_ds.get_tx_mode(),
VariantClassification.VT_SNP, "", "", str(loc), str(loc))
return chosen_tx, transcript_ds
def _get_chosen_tx_and_transcript_ds(self, chrom, loc):
config = TestUtils.createUnitTestConfig()
transcript_ds = TestUtils.createTranscriptProviderDatasource(config)
transcript_ds.set_tx_mode(TranscriptProvider.TX_MODE_CANONICAL)
start_txs = transcript_ds.get_transcripts_by_pos(chr=chrom, start=str(loc), end=str(loc))
chosen_tx = transcript_ds._choose_transcript(start_txs, transcript_ds.get_tx_mode(),
VariantClassification.VT_SNP, "", "", str(loc), str(loc))
return chosen_tx, transcript_ds
def test_retrieve_transcripts_from_region(self):
"""Test that we can retrieve a large number of transcripts. Requires a full gencode datasource."""
config = TestUtils.createUnitTestConfig()
transcript_ds = TestUtils.createTranscriptProviderDatasource(config)
filtered_txs = transcript_ds.get_transcripts_by_pos(chr="1", start="1", end="100000000")
self.assertTrue(len(filtered_txs) > 4000)
gene_set = set([tx.get_gene() for tx in filtered_txs])
self.assertTrue(len(gene_set) > 1500)
def test_retrieve_transcripts_from_region(self):
"""Test that we can retrieve a large number of transcripts. Requires a full gencode datasource."""
config = TestUtils.createUnitTestConfig()
transcript_ds = TestUtils.createTranscriptProviderDatasource(config)
filtered_txs = transcript_ds.get_transcripts_by_pos(chr="1", start="1", end="100000000")
self.assertTrue(len(filtered_txs) > 4000)
gene_set = set([tx.get_gene() for tx in filtered_txs])
self.assertTrue(len(gene_set) > 1500)
def test_3_prime_flank_annotation_negative_strand(self):
m = MutationDataFactory.default_create(chr="5",
start="1253255",
end="1253255",
ref_allele="A",
alt_allele="T",
build="hg19")
transcript_ds = TestUtils.createTranscriptProviderDatasource(
self.config)
m = transcript_ds.annotate_mutation(m)
self.assertEqual(m['variant_classification'], "3'Flank")
def test_not_5_prime_flank_annotation_positive_strand(self):
m = MutationDataFactory.default_create(chr="3",
start="180625088",
end="180625088",
ref_allele="C",
alt_allele="A",
build="hg19")
transcript_ds = TestUtils.createTranscriptProviderDatasource(
self.config)
m = transcript_ds.annotate_mutation(m)
self.assertEqual(m['variant_classification'], "IGR")
def test_appris_ccds_tag(self):
m = MutationDataFactory.default_create(chr="1",
start="200818757",
end="200818757",
ref_allele="C",
alt_allele="A",
build="hg19")
transcript_ds = TestUtils.createTranscriptProviderDatasource(
self.config)
m = transcript_ds.annotate_mutation(m)
tx = transcript_ds.get_transcript(m['annotation_transcript'])
self.assertTrue(
tx is not None,
"Transcript was None when it should have been found. Does the ground truth transcript above need to be updated?"
)
self.assertEqual(tx._transcript_id, 'ENST00000358823.2')
def test_protein_position_off_by_one(self, chrom, start, end, ref, alt, gt_prot_change):
config = TestUtils.createUnitTestConfig()
transcript_ds = TestUtils.createTranscriptProviderDatasource(config)
cc_txs_fp = file("testdata/tx_exact_uniprot_matches.txt", 'r')
cc_txs = [tx.rsplit(".", 1)[0] for tx in cc_txs_fp]
cc_txs.append("ENST00000338368") # Add a transcript that is not exactly the same, but close
cc_txs_fp.close()
transcript_ds.set_custom_canonical_txs(cc_txs)
m = MutationData()
m.chr = chrom
m.start = start
m.end = end
m.ref_allele = ref
m.alt_allele = alt
m2 = transcript_ds.annotate_mutation(m)
self.assertEqual(m2['protein_change'], gt_prot_change)
def test_protein_position_off_by_one(self, chrom, start, end, ref, alt, gt_prot_change):
config = TestUtils.createUnitTestConfig()
transcript_ds = TestUtils.createTranscriptProviderDatasource(config)
cc_txs_fp = file("testdata/tx_exact_uniprot_matches.txt", 'r')
cc_txs = [tx.rsplit(".", 1)[0] for tx in cc_txs_fp]
cc_txs.append("ENST00000338368") # Add a transcript that is not exactly the same, but close
cc_txs_fp.close()
transcript_ds.set_custom_canonical_txs(cc_txs)
m = MutationDataFactory.default_create()
m.chr = chrom
m.start = start
m.end = end
m.ref_allele = ref
m.alt_allele = alt
m2 = transcript_ds.annotate_mutation(m)
self.assertEqual(m2['protein_change'], gt_prot_change)
def test_3_prime_flank_annotation_negative_strand(self):
m = MutationDataFactory.default_create(chr="5", start="1253255", end="1253255", ref_allele="A", alt_allele="T", build="hg19")
transcript_ds = TestUtils.createTranscriptProviderDatasource(self.config)
m = transcript_ds.annotate_mutation(m)
self.assertEqual(m['variant_classification'], "3'Flank")
def test_not_5_prime_flank_annotation_positive_strand(self):
m = MutationDataFactory.default_create(chr="3", start="180625088", end="180625088", ref_allele="C", alt_allele="A", build="hg19")
transcript_ds = TestUtils.createTranscriptProviderDatasource(self.config)
m = transcript_ds.annotate_mutation(m)
self.assertEqual(m['variant_classification'], "IGR")