def test_run_snp_sites(self):
builder = SNPFeatureBuilder()
fasta_filename = os.path.join(test_data(), 'file_with_SNPs.aln')
with context_aware_tempdir() as output_directory:
stdout, stderr = builder._run_snp_sites('snp-sites', {},
fasta_filename,
output_directory)
expected_output_filename = os.path.join(output_directory, 'all_snps.vcf')
self.assertTrue(os.path.isfile(expected_output_filename))
def create_vcf_from_sequences(self):
with context_aware_tempfile('w', delete=False) as temp_fasta_file:
try:
self.vcf_input_file.remove()
except AttributeError:
# The file might have already been deleted or might not have been created
# by us so we shouldn't delete it.
pass
self.vcf_input_file = DeletableFile(
tempfile.NamedTemporaryFile('w', delete=False))
self.logger.info("Writing sequences to %s" % temp_fasta_file.name)
self._write_sequences(self.sequences.values(), temp_fasta_file)
temp_fasta_file.close()
self.vcf_input_file.close()
with context_aware_tempdir() as output_directory:
self.logger.info("Writing snps to %s" %
self.vcf_input_file.name)
self._run_snp_sites(self.snp_sites_exec,
{'-o': self.vcf_input_file.name},
temp_fasta_file.name, output_directory)
self.vcf_input_file = DeletableFile(
open(self.vcf_input_file.name, 'r'))
def context_aware_tempdir_mock(*args, **kwargs):
with context_aware_tempdir(*args, **kwargs) as tempdir:
folder_names.append(tempdir)
yield tempdir