def test_error_no_csq(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'no_csq.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
self.assertTrue('is not VEP-annotated. Please annotate the VCF with VEP before running this tool.' in str(context.exception))
def test_error_already_GX_annotated(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'input.gx.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
self.assertTrue('is already gene expression annotated. GX format header already exists.' in str(context.exception))
def test_error_more_than_one_sample_without_sample_name(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'multiple_samples.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
self.assertTrue('contains more than one sample. Please use the -s option to specify which sample to annotate.' in str(context.exception))
def test_error_custom_format_expression_column_not_set(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'input.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'custom',
'gene',
'-i', 'tracking_id',
]
vcf_expression_annotator.main(command)
self.assertTrue('--expression-column is not set. This is required when using the `custom` format.' == str(context.exception))
def test_error_more_than_one_sample_with_wrong_sample_name(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'multiple_samples.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
'-s', 'nonexistent_sample',
]
vcf_expression_annotator.main(command)
self.assertTrue('does not contain a sample column for sample nonexistent_sample.' in str(context.exception))
def test_stringtie_format_transcript_mode(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'transcripts.gtf'),
'stringtie',
'transcript',
]
vcf_expression_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.stringtie.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
temp_path.cleanup()
def test_kallisto_format_gene_mode(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'kallisto.genes'),
'kallisto',
'gene',
]
vcf_expression_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.kallisto.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
temp_path.cleanup()
def test_skip_variant_without_gene_in_csq(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.ensr_transcript.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.ensr_transcript.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
temp_path.cleanup()
def test_multiple_transcripts(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'multiple_transcripts.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'multiple_transcripts.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
temp_path.cleanup()
def test_mutation_without_matching_expression_value(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'no_matching_expression.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'no_matching_expression.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
temp_path.cleanup()
def test_warning_no_csq_for_variants(self):
with warnings.catch_warnings(record=True) as w:
command = [
os.path.join(self.test_data_dir, 'input.no_csq.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
self.assertEqual(len(w), 1)
self.assertTrue(issubclass(w[-1].category, Warning))
self.assertTrue("Variant is missing VEP annotation. INFO column doesn't contain CSQ field for variant" in str(w[-1].message))
def test_skip_ENSR_transcript(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.ensr_transcript.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'kallisto.transcripts'),
'kallisto',
'transcript',
]
vcf_expression_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.ensr_transcript.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
temp_path.cleanup()
def test_cufflinks_format_transcript_mode(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'isoforms.fpkm_tracking'),
'cufflinks',
'transcript',
]
vcf_expression_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.cufflinks.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
temp_path.cleanup()
def test_error_id_column_nonexistent_in_file(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'input.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'custom',
'gene',
'-i', 'nonexistent_column',
'-e', 'FPKM',
]
vcf_expression_annotator.main(command)
self.assertTrue('ERROR: id_column header nonexistent_column does not exist in expression_file' in str(context.exception))
def test_kallisto_with_transcript_version_in_expression_file(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'kallisto.transcript_version.transcripts'),
'kallisto',
'transcript',
"--ignore-transcript-version",
]
vcf_expression_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.kallisto.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
temp_path.cleanup()
def test_warning_no_csq_for_variants(self):
logging.disable(logging.NOTSET)
with LogCapture() as l:
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.no_csq.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
temp_path.cleanup()
l.check_present(('root', 'WARNING', S("Variant is missing VEP annotation. INFO column doesn't contain CSQ field for variant")))
def test_warning_mutation_without_matching_expression_value(self):
logging.disable(logging.NOTSET)
with LogCapture() as l:
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'no_matching_expression.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
temp_path.cleanup()
l.check_present(('root', 'WARNING', "1 of 1 transcripts did not have an expression entry for their gene id."))
def test_warning_kallisto_with_transcript_version_in_expression_file(self):
logging.disable(logging.NOTSET)
with LogCapture() as l:
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'kallisto.transcript_version.transcripts'),
'kallisto',
'transcript',
]
vcf_expression_annotator.main(command)
temp_path.cleanup()
l.check_present(('root', 'WARNING', "1 of 1 transcripts did not have an expression entry for their transcript id."))