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'])