def test_get_clusters_from_fasta_filepath_extending_reference_db(self): """ Correct clusters when clustering against db and adding new clusters """ clusters_res = get_clusters_from_fasta_filepath( self.tmp_unsorted_fasta_filepath, original_fasta_path=None, max_accepts=7, max_rejects=12, percent_ID=0.90, subject_fasta_filepath=self.ref_dna_seqs_fp, suppress_new_clusters=False, enable_rev_strand_matching=True, HALT_EXEC=False, save_uc_files=False) self.ref_test_clusters2.sort() self.ref_test_failures2.sort() self.ref_test_new_seeds2.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res, (self.ref_test_clusters2, self.ref_test_failures2, self.ref_test_new_seeds2))
def test_get_clusters_from_fasta_filepath_rev_strand_match(self): """ Test OTUs from filepath functions with rev strand match """ # seq and its rc don't cluster when enable_rev_strand_matching = False expected_cluster_list = [['uclust_test_seqs_0'], ['uclust_test_seqs_0_rc']] expected_failure_list = [] expected_new_seed_list = [ 'uclust_test_seqs_0', 'uclust_test_seqs_0_rc' ] clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_raw_dna_seqs_rc_filepath, original_fasta_path = None, save_uc_files=False, percent_ID = 0.90, enable_rev_strand_matching = False) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res, (expected_cluster_list, expected_failure_list, expected_new_seed_list)) # seq and its rc cluster when enable_rev_strand_matching = False expected_cluster_list = [[ 'uclust_test_seqs_0', 'uclust_test_seqs_0_rc' ]] expected_failure_list = [] expected_new_seed_list = ['uclust_test_seqs_0'] clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_raw_dna_seqs_rc_filepath, original_fasta_path = None, save_uc_files=False, percent_ID = 0.90, enable_rev_strand_matching = True) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res, (expected_cluster_list, expected_failure_list, expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_rev_strand_match(self): """ Test OTUs from filepath functions with rev strand match """ # seq and its rc don't cluster when enable_rev_strand_matching = False expected_cluster_list = [['uclust_test_seqs_0'], ['uclust_test_seqs_0_rc']] expected_failure_list = [] expected_new_seed_list = ['uclust_test_seqs_0', 'uclust_test_seqs_0_rc'] clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_raw_dna_seqs_rc_filepath, original_fasta_path = None, save_uc_files=False, percent_ID = 0.90, enable_rev_strand_matching = False) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res,(expected_cluster_list, expected_failure_list, expected_new_seed_list)) # seq and its rc cluster when enable_rev_strand_matching = False expected_cluster_list = [['uclust_test_seqs_0', 'uclust_test_seqs_0_rc']] expected_failure_list = [] expected_new_seed_list = ['uclust_test_seqs_0'] clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_raw_dna_seqs_rc_filepath, original_fasta_path = None, save_uc_files=False, percent_ID = 0.90, enable_rev_strand_matching = True) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res,(expected_cluster_list, expected_failure_list, expected_new_seed_list))
def test_get_clusters_from_fasta_filepath(self): """ Tests for return of lists of OTUs from given fasta filepath """ clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, \ original_fasta_path = None, percent_ID = 0.90, save_uc_files=False) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res,(expected_cluster_list, expected_failure_list, expected_new_seed_list))
def test_get_clusters_from_fasta_filepath(self): """ Tests for return of lists of OTUs from given fasta filepath """ clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, \ original_fasta_path = None, percent_ID = 0.90, save_uc_files=False) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res, (expected_cluster_list, expected_failure_list, expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_optimal(self): """ Test OTUs from filepath functions with optimal """ # need to compile a small test where optimal has an affect -- # this currently is only testing that we don't get a failure with # optimal clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, original_fasta_path = None, save_uc_files=False, percent_ID = 0.90, optimal = True) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res,(expected_cluster_list, expected_failure_list, expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_optimal(self): """ Test OTUs from filepath functions with optimal """ # need to compile a small test where optimal has an affect -- # this currently is only testing that we don't get a failure with # optimal clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, original_fasta_path = None, save_uc_files=False, percent_ID = 0.90, optimal = True) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res, (expected_cluster_list, expected_failure_list, expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_suppress_sort(self): """ Test OTUs from filepath functions with suppress sort """ expected = [['uclust_test_seqs_0'], ['uclust_test_seqs_1'], ['uclust_test_seqs_2'], ['uclust_test_seqs_3'], ['uclust_test_seqs_4'], ['uclust_test_seqs_5'], ['uclust_test_seqs_6', 'uclust_test_seqs_8'], ['uclust_test_seqs_7'], ['uclust_test_seqs_9']] clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, original_fasta_path = None, percent_ID = 0.90, suppress_sort = True, save_uc_files=False) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res,(expected_cluster_list, expected_failure_list, expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_suppress_sort(self): """ Test OTUs from filepath functions with suppress sort """ expected = [['uclust_test_seqs_0'], ['uclust_test_seqs_1'], ['uclust_test_seqs_2'], ['uclust_test_seqs_3'], ['uclust_test_seqs_4'], ['uclust_test_seqs_5'], ['uclust_test_seqs_6', 'uclust_test_seqs_8'], ['uclust_test_seqs_7'], ['uclust_test_seqs_9']] clusters_res = \ get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, original_fasta_path = None, percent_ID = 0.90, suppress_sort = True, save_uc_files=False) expected_cluster_list.sort() expected_failure_list.sort() expected_new_seed_list.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res, (expected_cluster_list, expected_failure_list, expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_extending_reference_db(self): """ Correct clusters when clustering against db and adding new clusters """ clusters_res = get_clusters_from_fasta_filepath( self.tmp_unsorted_fasta_filepath, original_fasta_path = None, max_accepts=7,max_rejects=12, percent_ID = 0.90, subject_fasta_filepath=self.ref_dna_seqs_fp, suppress_new_clusters=False,enable_rev_strand_matching=True, HALT_EXEC=False, save_uc_files=False) self.ref_test_clusters2.sort() self.ref_test_failures2.sort() self.ref_test_new_seeds2.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res,(self.ref_test_clusters2, self.ref_test_failures2, self.ref_test_new_seeds2))
def test_get_clusters_from_fasta_filepath_reference_db_only(self): """ Correct clusters returned when clustering against a database only """ clusters_res = get_clusters_from_fasta_filepath( self.tmp_unsorted_fasta_filepath, original_fasta_path = None, save_uc_files=False, max_accepts=7,max_rejects=12, percent_ID = 0.90, subject_fasta_filepath=self.ref_dna_seqs_fp, suppress_new_clusters=True, HALT_EXEC=False) self.ref_test_clusters1.sort() self.ref_test_failures1.sort() self.ref_test_new_seeds1.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res,(self.ref_test_clusters1, self.ref_test_failures1, self.ref_test_new_seeds1))
def test_get_clusters_from_fasta_filepath_reference_db_only(self): """ Correct clusters returned when clustering against a database only """ clusters_res = get_clusters_from_fasta_filepath( self.tmp_unsorted_fasta_filepath, original_fasta_path=None, save_uc_files=False, max_accepts=7, max_rejects=12, percent_ID=0.90, subject_fasta_filepath=self.ref_dna_seqs_fp, suppress_new_clusters=True, HALT_EXEC=False) self.ref_test_clusters1.sort() self.ref_test_failures1.sort() self.ref_test_new_seeds1.sort() clusters_res[0].sort() clusters_res[1].sort() clusters_res[2].sort() self.assertEqual(clusters_res, (self.ref_test_clusters1, self.ref_test_failures1, self.ref_test_new_seeds1))