def testBasicAnnotationWithChange(self):
""" Test whether we can translate from one coordinate system to another. This tests a known change.
"""
tDS = TranscriptToUniProtProteinPositionTransformingDatasource(title="UniProt", version="test", src_file="file://testdata/small_uniprot_prot_seq_ds/db")
# Must correspond to what the datasource is going to generate.
outputAnnotation = "UniProt_aapos"
m = MutationData()
m.createAnnotation('transcript_id', 'uc009vvt.1')
m.createAnnotation('protein_change', 'p.T1105A')
m = tDS.annotate_mutation(m)
self.assertTrue(m[outputAnnotation] == "969", "Did not get proper value (969): " + m[outputAnnotation])
def testBasicAnnotationNoChange(self):
""" Test whether we can translate from one coordinate system to another (v1). This tests no change.
"""
tDS = TranscriptToUniProtProteinPositionTransformingDatasource(title="UniProt", version="test", src_file="file://testdata/small_uniprot_prot_seq_ds/db")
# Must correspond to what the datasource is going to generate
outputAnnotation = "UniProt_aapos"
m = MutationDataFactory.default_create()
m.createAnnotation('transcript_id', 'uc003tqk.3')
m.createAnnotation('protein_change', 'p.S50T')
m = tDS.annotate_mutation(m)
self.assertTrue(m[outputAnnotation] == "50", "Did not get proper value (50): " + m[outputAnnotation])
def test_basic_annotation_with_change(self):
""" Test whether we can translate from one coordinate system to another (v2 2014). This tests a known change.
"""
tDS = TranscriptToUniProtProteinPositionTransformingDatasource(title="UniProt", version="test", src_file="file://testdata/small_uniprot_prot_seq_ds_blastp_2014/db")
# Must correspond to what the datasource is going to generate.
#ENST00000545482.1_Silent_p.S178S
outputAnnotation = "UniProt_aapos"
m = MutationDataFactory.default_create()
m.createAnnotation('transcript_id', 'ENST00000545482.1')
m.createAnnotation('protein_change', 'p.S178S')
m = tDS.annotate_mutation(m)
self.assertTrue(m[outputAnnotation] == "293", "Did not get proper value (293): " + m[outputAnnotation])
def testBasicAnnotationWithChange(self):
""" Test whether we can translate from one coordinate system to another (v1). This tests a known change.
"""
tDS = TranscriptToUniProtProteinPositionTransformingDatasource(
title="UniProt",
version="test",
src_file="file://testdata/small_uniprot_prot_seq_ds/db")
# Must correspond to what the datasource is going to generate.
outputAnnotation = "UniProt_aapos"
m = MutationData()
m.createAnnotation('transcript_id', 'uc009vvt.1')
m.createAnnotation('protein_change', 'p.T1105A')
m = tDS.annotate_mutation(m)
self.assertTrue(
m[outputAnnotation] == "969",
"Did not get proper value (969): " + m[outputAnnotation])
def testBasicAnnotationNoChange(self):
""" Test whether we can translate from one coordinate system to another (v1). This tests no change.
"""
tDS = TranscriptToUniProtProteinPositionTransformingDatasource(
title="UniProt",
version="test",
src_file="file://testdata/small_uniprot_prot_seq_ds/db")
# Must correspond to what the datasource is going to generate
outputAnnotation = "UniProt_aapos"
m = MutationDataFactory.default_create()
m.createAnnotation('transcript_id', 'uc003tqk.3')
m.createAnnotation('protein_change', 'p.S50T')
m = tDS.annotate_mutation(m)
self.assertTrue(
m[outputAnnotation] == "50",
"Did not get proper value (50): " + m[outputAnnotation])
def test_basic_annotation_no_change_2(self):
""" Test whether we can translate from one coordinate system to another (v2 ... 2014). This tests no change.
"""
tDS = TranscriptToUniProtProteinPositionTransformingDatasource(
title="UniProt",
version="test",
src_file="file://testdata/small_uniprot_prot_seq_ds_blastp_2014/db"
)
# Must correspond to what the datasource is going to generate
outputAnnotation = "UniProt_aapos"
m = MutationData()
m.createAnnotation('transcript_id', 'ENST00000264990.6')
m.createAnnotation('protein_change', 'p.S50T')
m = tDS.annotate_mutation(m)
self.assertTrue(
m[outputAnnotation] == "50",
"Did not get proper value (50): " + m[outputAnnotation])
def test_basic_annotation_with_change(self):
""" Test whether we can translate from one coordinate system to another (v2 2014). This tests a known change.
"""
tDS = TranscriptToUniProtProteinPositionTransformingDatasource(
title="UniProt",
version="test",
src_file="file://testdata/small_uniprot_prot_seq_ds_blastp_2014/db"
)
# Must correspond to what the datasource is going to generate.
#ENST00000545482.1_Silent_p.S178S
outputAnnotation = "UniProt_aapos"
m = MutationData()
m.createAnnotation('transcript_id', 'ENST00000545482.1')
m.createAnnotation('protein_change', 'p.S178S')
m = tDS.annotate_mutation(m)
self.assertTrue(
m[outputAnnotation] == "293",
"Did not get proper value (293): " + m[outputAnnotation])
