def testRealWorld(self):
"""Test that the full COSMIC datasource can retrieve entries by both gp and gpp."""
gafDS = TestUtils.createTranscriptProviderDatasource(self.config)
cosmicDS = TestUtils.createCosmicDatasource(self.config)
# These values are not taken from a real world scenario, but are cooked for this test.
m = MutationData()
m.chr = '1'
m.start = '12941796'
m.end = '12941796'
m.ref_allele = "G"
m.alt_allele = "T"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '0')
#1 150483621 150483621
m = MutationData()
m.chr = '1'
m.start = '150483621'
m.end = '150483621'
m.ref_allele = "G"
m.alt_allele = "T"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
def testRealWorld(self):
"""Test that the full COSMIC datasource can retrieve entries by both gp and gpp."""
gafDS = TestUtils.createTranscriptProviderDatasource(self.config)
cosmicDS = TestUtils.createCosmicDatasource(self.config)
# These values are not taken from a real world scenario, but are cooked for this test.
m = MutationDataFactory.default_create()
m.chr = '1'
m.start = '12941796'
m.end = '12941796'
m.ref_allele = "G"
m.alt_allele = "T"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '0')
#1 150483621 150483621
m = MutationDataFactory.default_create()
m.chr = '1'
m.start = '150483621'
m.end = '150483621'
m.ref_allele = "G"
m.alt_allele = "T"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
def testRealWorld(self):
"""Test that the full COSMIC datasource can retrieve entries by both gp and gpp."""
gafDS = TestUtils.createTranscriptProviderDatasource(self.config)
cosmicDS = TestUtils.createCosmicDatasource(self.config)
# These values are not taken from a real world scenario, but are cooked for this test.
m = MutationDataFactory.default_create()
m.chr = '1'
m.start = '12941796'
m.end = '12941796'
m.ref_allele = "G"
m.alt_allele = "T"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '0')
# # 7:140481411-140481411
m = MutationDataFactory.default_create()
m.chr = '7'
m.start = '140481411'
m.end = '140481411'
m.ref_allele = "G"
m.alt_allele = "T"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
# As a reminder, the COSMIC datasource does not check the ref and alt allele for a match. (14)
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '22')
# # 7:140481411-140481411
m = MutationDataFactory.default_create()
m.chr = '7'
m.start = '140481411'
m.end = '140481411'
m.ref_allele = "G"
m.alt_allele = "A"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
# As a reminder, the COSMIC datasource does not check the ref and alt allele for a match. (7)
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '22')
# Test a gpp record
m = MutationDataFactory.default_create()
m.createAnnotation("gene", "ABL1")
m.createAnnotation("transcript_protein_position_start", "255")
m.createAnnotation("transcript_protein_position_end", "255")
# These values (chr, start, and end) are incorrect. This is by design -- just being used as dummy values.
m.chr = '9'
m.start = '1'
m.end = '1'
m = cosmicDS.annotate_mutation(m)
# $ grep -P "^ABL1\t" ~/broad_oncotator_configs/CosmicCompleteTargetedScreensMutantExport.tsv/v76/CosmicCompleteTargetedScreensMutantExport.tsv | cut -f 19,24 | sort | egrep "[A-Z]255[A-Z]" | wc
# 157
#
# The rest:
# $ grep -P "^ABL1\t" ~/broad_oncotator_configs/CosmicCompleteTargetedScreensMutantExport.tsv/v76/CosmicCompleteTargetedScreensMutantExport.tsv | cut -f 19,24 | sort | uniq | egrep "_"
# p.H295_P296insH 9:133747575-133747576
# p.K356_K357insE 9:133748407-133748408
# p.K357_N358insK 9:133748407-133748408
# p.L184_K274del 9:133738150-133738422
# p.L248_K274del
#
# $ grep -P "^ABL1\t" ~/broad_oncotator_configs/CosmicCompleteTargetedScreensMutantExport.tsv/v76/CosmicCompleteTargetedScreensMutantExport.tsv | cut -f 19,24 | sort | egrep "_K274"
# p.L184_K274del 9:133738150-133738422
# p.L184_K274del 9:133738150-133738422
# p.L248_K274del
# p.L248_K274del
#
# four overlap p.255 + 157 that are exact matches for p.255.
# 155 + 4 were hematopoietic_and_lymphoid_tissue
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == str(157 + 4))
self.assertTrue(m['COSMIC_overlapping_mutation_AAs'].find('255') != -1)
self.assertTrue(
m['COSMIC_overlapping_mutation_AAs'].find('p.L184_K274del') != -1)
self.assertTrue(
m['COSMIC_overlapping_mutation_AAs'].find('p.L248_K274del') != -1)
self.assertTrue(
m['COSMIC_overlapping_primary_sites'].find(
"haematopoietic_and_lymphoid_tissue(159)") != -1,
"Did not have the correct primary sites annotation (haematopoietic_and_lymphoid_tissue(159)): "
+ m['COSMIC_overlapping_primary_sites'])
def testRealWorld(self):
"""Test that the full COSMIC datasource can retrieve entries by both gp and gpp."""
gafDS = TestUtils.createTranscriptProviderDatasource(self.config)
cosmicDS = TestUtils.createCosmicDatasource(self.config)
# These values are not taken from a real world scenario, but are cooked for this test.
m = MutationDataFactory.default_create()
m.chr = '1'
m.start = '12941796'
m.end = '12941796'
m.ref_allele = "G"
m.alt_allele = "T"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '0')
# # 7:140481411-140481411
m = MutationDataFactory.default_create()
m.chr = '7'
m.start = '140481411'
m.end = '140481411'
m.ref_allele = "G"
m.alt_allele = "T"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
# As a reminder, the COSMIC datasource does not check the ref and alt allele for a match. (14)
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '22')
# # 7:140481411-140481411
m = MutationDataFactory.default_create()
m.chr = '7'
m.start = '140481411'
m.end = '140481411'
m.ref_allele = "G"
m.alt_allele = "A"
m = gafDS.annotate_mutation(m)
m = cosmicDS.annotate_mutation(m)
# As a reminder, the COSMIC datasource does not check the ref and alt allele for a match. (7)
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '22')
# Test a gpp record
m = MutationDataFactory.default_create()
m.createAnnotation("gene", "ABL1")
m.createAnnotation("transcript_protein_position_start", "255")
m.createAnnotation("transcript_protein_position_end", "255")
# These values (chr, start, and end) are incorrect. This is by design -- just being used as dummy values.
m.chr = '9'
m.start = '1'
m.end = '1'
m = cosmicDS.annotate_mutation(m)
# $ grep -P "^ABL1\t" ~/broad_oncotator_configs/CosmicCompleteTargetedScreensMutantExport.tsv/v76/CosmicCompleteTargetedScreensMutantExport.tsv | cut -f 19,24 | sort | egrep "[A-Z]255[A-Z]" | wc
# 157
#
# The rest:
# $ grep -P "^ABL1\t" ~/broad_oncotator_configs/CosmicCompleteTargetedScreensMutantExport.tsv/v76/CosmicCompleteTargetedScreensMutantExport.tsv | cut -f 19,24 | sort | uniq | egrep "_"
# p.H295_P296insH 9:133747575-133747576
# p.K356_K357insE 9:133748407-133748408
# p.K357_N358insK 9:133748407-133748408
# p.L184_K274del 9:133738150-133738422
# p.L248_K274del
#
# $ grep -P "^ABL1\t" ~/broad_oncotator_configs/CosmicCompleteTargetedScreensMutantExport.tsv/v76/CosmicCompleteTargetedScreensMutantExport.tsv | cut -f 19,24 | sort | egrep "_K274"
# p.L184_K274del 9:133738150-133738422
# p.L184_K274del 9:133738150-133738422
# p.L248_K274del
# p.L248_K274del
#
# four overlap p.255 + 157 that are exact matches for p.255.
# 155 + 4 were hematopoietic_and_lymphoid_tissue
self.assertTrue(m['COSMIC_n_overlapping_mutations'] == str(157 + 4))
self.assertTrue(m['COSMIC_overlapping_mutation_AAs'].find('255') != -1)
self.assertTrue(m['COSMIC_overlapping_mutation_AAs'].find('p.L184_K274del') != -1)
self.assertTrue(m['COSMIC_overlapping_mutation_AAs'].find('p.L248_K274del') != -1)
self.assertTrue(m['COSMIC_overlapping_primary_sites'].find("haematopoietic_and_lymphoid_tissue(159)") != -1, "Did not have the correct primary sites annotation (haematopoietic_and_lymphoid_tissue(159)): " + m['COSMIC_overlapping_primary_sites'])
