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)