def test_export(self):
rf = RandomForestClassifier()
rf.fit(np.array([[0, 1]]), np.array(['cluster_1']))
classifier = SampleClassifier(rf, np.array(['feature_1', 'feature_2']))
classifier.logger = MagicMock()
with context_aware_tempfile('w', delete=False) as output_file:
classifier.export(output_file)
output_file.close()
input_file = open(output_file.name, 'r')
new_classifier = SampleClassifier.load(input_file, force=True)
################################################################################
## Uncomment me if you want to create a new classifier test file. Remember to
## update the md5sum and sha256sum values in the test_load function above
## afterwards even if you haven't changed how the classifier is created.
################################################################################
#
# path_to_classifier = os.path.join(test_data(), 'classifier.pkl')
# with open(path_to_classifier, 'wb') as output_file:
# classifier.export(output_file)
#
################################################################################
self.assertIsInstance(new_classifier.classifier,
RandomForestClassifier)
assert_array_equal(new_classifier.feature_labels,
np.array(['feature_1', 'feature_2']))
def test_create_vcf_from_sequences_does_not_delete_existing(self, os_mock):
builder = SNPFeatureBuilder()
os_mock.remove.side_effect = os.remove
with context_aware_tempfile('w', delete=False) as temp_vcf_file:
builder.vcf_input_file = temp_vcf_file
fasta_filename = os.path.join(test_data(), 'file_with_SNPs.aln')
fasta_file = open(fasta_filename, 'r')
builder.load_fasta_sequences(fasta_file)
builder.create_vcf_from_sequences()
self.assertFalse(temp_vcf_file.name in os_mock.remove.call_args_list)
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_tempfile_mock(*args, **kwargs):
with context_aware_tempfile(*args, **kwargs) as tempfile:
filenames.append(tempfile.name)
yield tempfile
