def test_write_seqrep_data_to_file(self):
'''test write_seqrep_data_to_file'''
finder = data_finder.DataFinder(ini_file, self.pipeline_root)
tmpfile = 'tmp.data_finder.write_seqrep_data_to_file.out'
expected_file = os.path.join(data_dir, 'write_seqrep_data_to_file.tsv')
tmp_expected = 'tmp.data_finder.write_seqrep_data_to_file.expect'
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
finder.write_seqrep_data_to_file(tmpfile)
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def test_write_pipeline_data_to_file_mykrobe_predict_pipeline(self):
'''test write_pipeline_data_to_file for mykrobe_predict pipeline'''
finder = data_finder.DataFinder(ini_file, self.pipeline_root)
tmpfile = 'tmp.data_finder.write_pipeline_data_to_file.mykrobe_predict.out'
finder.write_pipeline_data_to_file(tmpfile, 'mykrobe_predict')
expected_file = os.path.join(
data_dir, 'write_pipeline_data_to_file.mykrobe_predict.tsv')
tmp_expected = 'tmp.data_finder.write_pipeline_data_to_file.mykrobe_predict.expect'
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def test_write_pipeline_data_to_file_variant_call_pipeline(self):
'''test write_pipeline_data_to_file for variant_call pipeline'''
finder = data_finder.DataFinder(ini_file, self.pipeline_root)
tmpfile = 'tmp.data_finder.write_pipeline_data_to_file.variant_call.out'
finder.write_pipeline_data_to_file(tmpfile, 'variant_call')
expected_file = os.path.join(
data_dir, 'write_pipeline_data_to_file.variant_call.tsv')
tmp_expected = 'tmp.data_finder.write_pipeline_data_to_file.variant_call.expect'
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def test_write_pipeline_data_to_file_variant_call_pipeline(self):
"""test write_pipeline_data_to_file for variant_call pipeline"""
finder = data_finder.DataFinder(ini_file, self.pipeline_root)
tmpfile = "tmp.data_finder.write_pipeline_data_to_file.variant_call.out"
finder.write_pipeline_data_to_file(tmpfile, "variant_call")
expected_file = os.path.join(
data_dir, "write_pipeline_data_to_file.variant_call.tsv")
tmp_expected = "tmp.data_finder.write_pipeline_data_to_file.variant_call.expect"
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def test_write_pipeline_data_to_file_remove_contam_pipeline(self):
"""test write_pipeline_data_to_file for remove_contam pipeline"""
finder = data_finder.DataFinder(ini_file, self.pipeline_root)
tmpfile = "tmp.data_finder.write_pipeline_data_to_file.remove_contam.out"
expected_file = os.path.join(
data_dir, "write_pipeline_data_to_file.remove_contam.tsv")
tmp_expected = (
"tmp.data_finder.write_pipeline_data_to_file.remove_contam.expect")
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
finder.write_pipeline_data_to_file(tmpfile, "remove_contam")
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def test_write_pipeline_data_to_file_mykrobe_predict_pipeline(self):
"""test write_pipeline_data_to_file for mykrobe_predict pipeline"""
finder = data_finder.DataFinder(ini_file, self.pipeline_root)
tmpfile = "tmp.data_finder.write_pipeline_data_to_file.mykrobe_predict.out"
finder.write_pipeline_data_to_file(tmpfile, "mykrobe_predict")
expected_file = os.path.join(
data_dir, "write_pipeline_data_to_file.mykrobe_predict.tsv")
tmp_expected = (
"tmp.data_finder.write_pipeline_data_to_file.mykrobe_predict.expect"
)
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def test_write_seqrep_data_to_file_dataset_option(self):
"""test write_seqrep_data_to_file limit to one dataset"""
finder = data_finder.DataFinder(ini_file,
self.pipeline_root,
dataset_name="set2")
tmpfile = "tmp.data_finder.write_seqrep_data_to_file.set2.out"
expected_file = os.path.join(data_dir,
"write_seqrep_data_to_file.set2.tsv")
tmp_expected = "tmp.data_finder.write_seqrep_data_to_file.set2.expect"
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
finder.write_seqrep_data_to_file(tmpfile)
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def test_write_pipeline_data_to_file_remove_contam_pipeline_reference_option(
self):
'''test write_pipeline_data_to_file for remove_contam pipeline use reference option'''
finder = data_finder.DataFinder(ini_file, self.pipeline_root)
tmpfile = 'tmp.data_finder.write_pipeline_data_to_file.remove_contam.ref.1.out'
expected_file = os.path.join(
data_dir, 'write_pipeline_data_to_file.remove_contam.ref.1.tsv')
tmp_expected = 'tmp.data_finder.write_pipeline_data_to_file.remove_contam.ref.1.expect'
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
finder.write_pipeline_data_to_file(tmpfile,
'remove_contam',
reference_id=1)
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def test_write_pipeline_data_to_file_remove_contam_pipeline_dataset_option(
self):
'''test write_pipeline_data_to_file for remove_contam pipeline limit to one dataset'''
finder = data_finder.DataFinder(ini_file,
self.pipeline_root,
dataset_name='set2')
tmpfile = 'tmp.data_finder.write_pipeline_data_to_file.remove_contam.set2.out'
expected_file = os.path.join(
data_dir, 'write_pipeline_data_to_file.remove_contam.set2.tsv')
tmp_expected = 'tmp.data_finder.write_pipeline_data_to_file.remove_contam.set2.expect'
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
finder.write_pipeline_data_to_file(tmpfile, 'remove_contam')
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)
def run(options):
finder = data_finder.DataFinder(
options.db_config_file,
options.pipeline_root,
include_withdrawn=options.include_withdrawn,
include_internal_ids=options.include_internal_ids,
dataset_name=options.dataset_name)
if options.pipeline:
finder.write_pipeline_data_to_file(
options.outfile,
options.pipeline,
pipeline_version=options.pipeline_version,
reference_id=options.reference_id)
else:
finder.write_seqrep_data_to_file(options.outfile)
def test_write_pipeline_data_to_file_remove_contam_pipeline_with_internal_ids(
self):
'''test write_pipeline_data_to_file for remove_contam pipeline with internal ids'''
finder = data_finder.DataFinder(ini_file,
self.pipeline_root,
include_internal_ids=True)
tmpfile = 'tmp.data_finder.write_pipeline_data_to_file.remove_contam.with_internal_ids.out'
expected_file = os.path.join(
data_dir,
'write_pipeline_data_to_file.remove_contam.with_internal_ids.tsv')
tmp_expected = 'tmp.data_finder.write_pipeline_data_to_file.remove_contam.expect'
fix_pipeline_root_in_file(expected_file, tmp_expected,
self.pipeline_root)
finder.write_pipeline_data_to_file(tmpfile, 'remove_contam')
self.assertTrue(filecmp.cmp(tmp_expected, tmpfile, shallow=False))
os.unlink(tmpfile)
os.unlink(tmp_expected)