def testMixedAnnotation(self): """Test that the COSMIC datasource can retrieve entries by both gp and gpp.""" tabixDir = "testdata/small_cosmic_with_gp_and_gpp/" cosmicDS = Cosmic( src_file=tabixDir + "small_cosmic_trimmed_for_sorting.txt.tbi.gz", title="Cosmic", version="test", gpp_tabix_file=tabixDir + "small_cosmic_trimmed_for_sorting.txt.tbi.byAA.sorted.tsv.gz") # These values are not taken from a real world scenario, but are cooked for this test. # Line 9 should get picked up genomic coords # Lines 7,8 should get picked up by the protein position m = MutationDataFactory.default_create() m.createAnnotation("gene", "A2M") m.createAnnotation("transcript_protein_position_start", "1300") m.createAnnotation("transcript_protein_position_end", "1400") m.chr = '12' m.start = '9227220' m.end = '9227230' m = cosmicDS.annotate_mutation(m) self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '3') self.assertTrue( m['COSMIC_overlapping_mutation_AAs'].find('1229') != -1, "Could not find the entry specified by genomic coords.") self.assertTrue( m['COSMIC_overlapping_primary_sites'] == "lung(3)", "Did not have the correct primary sites annotation (lung(3)): " + m['COSMIC_overlapping_primary_sites'])
def testBasicAnnotate(self): '''Test that the COSMIC datasource can be initialized with two index files (gp and gpp) and a simple annotation performed''' tabixDir = "testdata/small_cosmic_with_gp_and_gpp/" cosmicDS = Cosmic(src_file=tabixDir + "small_cosmic_trimmed_for_sorting.txt.tbi.gz", title="Cosmic", version="test", gpp_tabix_file= tabixDir + "small_cosmic_trimmed_for_sorting.txt.tbi.byAA.sorted.tsv.gz") # These values are not taken from a real world scenario, but are cooked for this test. m = MutationDataFactory.default_create() m.createAnnotation("gene", "EGFR") m.createAnnotation("transcript_protein_position_start", "747") m.createAnnotation("transcript_protein_position_end", "747") m.chr = '7' m.start = '55259560' m.end = '55259560' m = cosmicDS.annotate_mutation(m) self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '2')
def testBasicAnnotate(self): '''Test that the COSMIC datasource can be initialized with two index files (gp and gpp) and a simple annotation performed''' tabixDir = "testdata/small_cosmic_with_gp_and_gpp/" cosmicDS = Cosmic(src_file=tabixDir + "small_cosmic_trimmed_for_sorting.txt.tbi.gz", title="Cosmic", version="test", gpp_tabix_file= tabixDir + "small_cosmic_trimmed_for_sorting.txt.tbi.byAA.sorted.tsv.gz") # These values are not taken from a real world scenario, but are cooked for this test. m = MutationDataFactory.default_create() m.createAnnotation("gene", "EGFR") m.createAnnotation("transcript_protein_position_start", "747") m.createAnnotation("transcript_protein_position_end", "747") m.chr = '7' m.start = '55259560' m.end = '55259560' m = cosmicDS.annotate_mutation(m) self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '2')
def testMixedAnnotation(self): """Test that the COSMIC datasource can retrieve entries by both gp and gpp.""" tabixDir = "testdata/small_cosmic_with_gp_and_gpp/" cosmicDS = Cosmic(src_file=tabixDir + "small_cosmic_trimmed_for_sorting.txt.tbi.gz", title="Cosmic", version="test", gpp_tabix_file= tabixDir + "small_cosmic_trimmed_for_sorting.txt.tbi.byAA.sorted.tsv.gz") # These values are not taken from a real world scenario, but are cooked for this test. # Line 9 should get picked up genomic coords # Lines 7,8 should get picked up by the protein position m = MutationDataFactory.default_create() m.createAnnotation("gene", "A2M") m.createAnnotation("transcript_protein_position_start", "1300") m.createAnnotation("transcript_protein_position_end", "1400") m.chr = '12' m.start = '9227220' m.end = '9227230' m = cosmicDS.annotate_mutation(m) self.assertTrue(m['COSMIC_n_overlapping_mutations'] == '3') self.assertTrue(m['COSMIC_overlapping_mutation_AAs'].find('1229') != -1, "Could not find the entry specified by genomic coords.") self.assertTrue(m['COSMIC_overlapping_primary_sites'] == "lung(3)", "Did not have the correct primary sites annotation (lung(3)): " + m['COSMIC_overlapping_primary_sites'])