#!/usr/bin/env python """ provides unit tests for the usearch.py module """ __author__ = "William Walters" __copyright__ = "Copyright 2007-2012, The Cogent Project" __credits__ = ["William Walters", "Jose Carlos Clemente Litran", "Greg Caporaso"] __license__ = "GPL" __version__ = "1.5.3" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" __status__ = "Production" from os.path import isfile, basename, join, exists from shutil import rmtree from glob import glob from cogent.util.misc import remove_files from cogent.util.unit_test import TestCase, main from cogent.app.util import ApplicationError, get_tmp_filename from cogent.util.misc import create_dir, get_random_directory_name from cogent.app.usearch import (Usearch, clusters_from_blast_uc_file, usearch_fasta_sort_from_filepath, usearch_dereplicate_exact_subseqs, usearch_dereplicate_exact_seqs, usearch_sort_by_abundance, usearch_cluster_error_correction, usearch_chimera_filter_de_novo, usearch_chimera_filter_ref_based, usearch_cluster_seqs, enumerate_otus, assign_reads_to_otus, usearch_qf, concatenate_fastas, get_retained_chimeras, assign_dna_reads_to_protein_database, assign_dna_reads_to_dna_database,) __author__ = "William Walters" __copyright__ = "Copyright 2007-2009, The Cogent Project" __credits__ = ["William Walters"] __license__ = "GPL" __version__ = "1.6.0.dev" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" __status__ = "Development" class UsearchTests(TestCase): def setUp(self): # create the temporary input files self.dna_seqs_1 = dna_seqs_1 self.dna_seqs_2 = dna_seqs_usearch self.dna_seqs_3 = dna_seqs_3 self.dna_seqs_4 = dna_seqs_4 self.protein_ref_seqs1 = protein_ref_seqs1 self.ref_database = usearch_ref_seqs1 self.dna_seqs_with_abundance = dna_seqs_with_abundance self.de_novo_chimera_seqs = de_novo_chimera_seqs self.dna_seqs_with_dups = dna_seqs_with_dups self.dna_seqs_reference_otu_picking = dna_seqs_reference_otu_picking # Expected output files self.uc_lines1 = uc_lines1 self.expected_otu_assignments = expected_otu_assignments self.expected_enumerated_fasta = expected_enumerated_fasta self.expected_enumerated_fasta_added_options =\ expected_enumerated_fasta_added_options self.expected_clusters_w_abundance_default_settings =\ expected_clusters_w_abundance_default_settings self.expected_clusters_w_abundance_low_setting =\ expected_clusters_w_abundance_low_setting self.expected_reference_filtered_seqs =\ expected_reference_filtered_seqs self.expected_de_novo_chimeras_default =\ expected_de_novo_chimeras_default self.expected_de_novo_chimera_filtered_skew11 =\ expected_de_novo_chimera_filtered_skew11 self.expected_cluster_err_seqs =\ expected_cluster_err_seqs self.expected_sorted_by_abundance_no_filter =\ expected_sorted_by_abundance_no_filter self.expected_derep_seqs = expected_derep_seqs self.expected_abundance_sort_filtered = expected_abundance_sort_filtered self.expected_len_sorted_seqs = expected_len_sorted_seqs self.expected_combined_dna_seqs_1_seqs_usearch =\ expected_combined_dna_seqs_1_seqs_usearch self.retained_chimeras_seqs1 = retained_chimeras_seqs1 self.retained_chimeras_seqs2 = retained_chimeras_seqs2 self.expected_retained_chimeras_union =\ expected_retained_chimeras_union self.expected_retained_chimeras_intersection =\ expected_retained_chimeras_intersection self.expected_derep_seqs_full_len =\ expected_derep_seqs_full_len # Create temporary files for use with unit tests self.tmp_dir = '/tmp/' self.tmp_seq_filepath1 = get_tmp_filename(\ prefix='UsearchOtuPickerTest_',\ suffix='.fasta') seq_file = open(self.tmp_seq_filepath1,'w') seq_file.write(self.dna_seqs_1) seq_file.close() self.tmp_seq_filepath2 = get_tmp_filename(\ prefix='UsearchOtuPickerTest_',\ suffix='.fasta') seq_file = open(self.tmp_seq_filepath2,'w') seq_file.write(self.dna_seqs_2) seq_file.close() self.dna_seqs3_filepath = get_tmp_filename(\ prefix='UsearchOtuPickerTest_',\ suffix='.fasta') seq_file = open(self.dna_seqs3_filepath,'w') seq_file.write(self.dna_seqs_3) seq_file.close() self.dna_seqs4_filepath = get_tmp_filename(\ prefix='UsearchOtuPickerTest_',\ suffix='.fasta') seq_file = open(self.dna_seqs4_filepath,'w') seq_file.write(self.dna_seqs_4) seq_file.close() self.protein_ref_seqs1_filepath = get_tmp_filename(\ prefix='UsearchOtuPickerTest_',\ suffix='.fasta') seq_file = open(self.protein_ref_seqs1_filepath,'w') seq_file.write(self.protein_ref_seqs1) seq_file.close() self.tmp_ref_database = get_tmp_filename(\ prefix='UsearchRefDatabase_',\ suffix='.fasta') seq_file = open(self.tmp_ref_database, 'w') seq_file.write(self.ref_database) seq_file.close() self.tmp_seqs_w_abundance = get_tmp_filename(\ prefix='UsearchSeqsAbundance_',\ suffix='.fasta') seq_file = open(self.tmp_seqs_w_abundance, 'w') seq_file.write(self.dna_seqs_with_abundance) seq_file.close() self.tmp_de_novo_chimera_seqs = get_tmp_filename(\ prefix='UsearchdenovoChimera_',\ suffix='.fasta') seq_file = open(self.tmp_de_novo_chimera_seqs, 'w') seq_file.write(self.de_novo_chimera_seqs) seq_file.close() self.tmp_dna_seqs_with_dups = get_tmp_filename(\ prefix='UsearchDupDNASeqs_',\ suffix='.fasta') seq_file = open(self.tmp_dna_seqs_with_dups, 'w') seq_file.write(self.dna_seqs_with_dups) seq_file.close() self.tmp_retained_chimeras_seqs1 = get_tmp_filename(\ prefix="UsearchRetainedChimeras1_",\ suffix=".fasta") seq_file = open(self.tmp_retained_chimeras_seqs1, 'w') seq_file.write(self.retained_chimeras_seqs1) seq_file.close() self.tmp_retained_chimeras_seqs2 = get_tmp_filename(\ prefix="UsearchRetainedChimeras1_",\ suffix=".fasta") seq_file = open(self.tmp_retained_chimeras_seqs2, 'w') seq_file.write(self.retained_chimeras_seqs2) seq_file.close() self.tmp_dna_seqs_ref_otu_picking = get_tmp_filename(\ prefix="UsearchRefOtuPicking_",\ suffix=".fasta") seq_file = open(self.tmp_dna_seqs_ref_otu_picking, "w") seq_file.write(self.dna_seqs_reference_otu_picking) seq_file.close() self._files_to_remove =\ [self.tmp_seq_filepath1, self.tmp_seq_filepath2, self.tmp_ref_database, self.tmp_seqs_w_abundance, self.tmp_de_novo_chimera_seqs, self.tmp_dna_seqs_with_dups, self.tmp_retained_chimeras_seqs1, self.tmp_retained_chimeras_seqs2, self.tmp_dna_seqs_ref_otu_picking, self.dna_seqs3_filepath, self.protein_ref_seqs1_filepath, self.dna_seqs4_filepath] self._dirs_to_remove = [] def tearDown(self): remove_files(self._files_to_remove) if self._dirs_to_remove: for curr_dir in self._dirs_to_remove: rmtree(curr_dir) def test_usearch_qf(self): """ Main program loop test, with default parameters """ # cluster size filtering set to 1 instead of default 4 clusters, failures = usearch_qf(self.tmp_seq_filepath2, output_dir = self.tmp_dir, db_filepath = self.tmp_ref_database, minsize = 1, remove_usearch_logs=True, chimeras_retention = 'intersection') expected_clusters = {'1': ['Solemya', 'Solemya_seq2'], '0': ['usearch_ecoli_seq', 'usearch_ecoli_seq2']} expected_failures = ['chimera'] self.assertEqual(clusters, expected_clusters) self.assertEqual(failures, expected_failures) def test_usearch_qf_minlen(self): """ Main program loop test, with longer minlen """ # cluster size filtering set to 1 instead of default 4 clusters, failures = usearch_qf(self.tmp_seq_filepath2, output_dir = self.tmp_dir, db_filepath = self.tmp_ref_database, minsize = 1, remove_usearch_logs=True, chimeras_retention = 'intersection', minlen=110) expected_clusters = {'0': ['usearch_ecoli_seq', 'usearch_ecoli_seq2']} expected_failures = ['Solemya', 'Solemya_seq2', 'chimera'] self.assertEqual(clusters, expected_clusters) self.assertEqual(failures, expected_failures) def test_usearch_qf_reference_otu_picking(self): """ Main program loop test, with reference + new clusters """ # cluster size filtering set to 1 instead of default 4 clusters, failures = usearch_qf(self.tmp_dna_seqs_ref_otu_picking, output_dir = self.tmp_dir, refseqs_fp = self.tmp_ref_database, reference_chimera_detection=False, minsize = 1, remove_usearch_logs=True, suppress_new_clusters=False) # Will cluster everything including RandomCrap, as new clusters allowed. expected_clusters = {'1': ['Solemya', 'Solemya_seq2'], '0': ['usearch_ecoli_seq', 'usearch_ecoli_seq2'], '2': ['RandomCrap']} expected_failures = [] self.assertEqual(clusters, expected_clusters) self.assertEqual(failures, expected_failures) def test_usearch_qf_reference_otu_picking_no_new_clusters(self): """ Main program loop test, with reference and no new clusters """ # cluster size filtering set to 1 instead of default 4 clusters, failures = usearch_qf(self.tmp_dna_seqs_ref_otu_picking, output_dir = self.tmp_dir, refseqs_fp = self.tmp_ref_database, reference_chimera_detection=False, minsize = 1, remove_usearch_logs=True, suppress_new_clusters=True) # Will cluster everything but RandomCrap, as no new clusters allowed. expected_clusters = {'1': ['Solemya', 'Solemya_seq2'], '0': ['usearch_ecoli_seq', 'usearch_ecoli_seq2']} expected_failures = ['RandomCrap'] self.assertEqual(clusters, expected_clusters) self.assertEqual(failures, expected_failures) def test_usearch_qf_no_ref_database(self): """ Main program loop with no reference chimera testing """ # cluster size filtering set to 1 instead of default 4 clusters, failures = usearch_qf(self.tmp_seq_filepath2, output_dir = self.tmp_dir, reference_chimera_detection=False, minsize = 1, remove_usearch_logs=True) # Chimera sequence should not be detected without reference test. expected_clusters = {'1': ['Solemya', 'Solemya_seq2'], '0': ['usearch_ecoli_seq', 'usearch_ecoli_seq2'], '2': ['chimera']} expected_failures = [] self.assertEqual(clusters, expected_clusters) self.assertEqual(failures, expected_failures) def test_usearch_qf_union(self): """ Main program loop with union nonchimera retention """ # cluster size filtering set to 1 instead of default 4 clusters, failures = usearch_qf(self.tmp_seq_filepath2, output_dir = self.tmp_dir, reference_chimera_detection=False, minsize = 1, remove_usearch_logs=True, chimeras_retention = 'union') # Chimera sequence retained as passes de novo test expected_clusters = {'1': ['Solemya', 'Solemya_seq2'], '0': ['usearch_ecoli_seq', 'usearch_ecoli_seq2'], '2': ['chimera']} expected_failures = [] self.assertEqual(clusters, expected_clusters) self.assertEqual(failures, expected_failures) def test_usearch_qf_disabled_filters(self): """ Returns expected clustering with no filtering """ # cluster size filtering set to 1 instead of default 4 clusters, failures = usearch_qf(self.tmp_seq_filepath2, output_dir = self.tmp_dir, de_novo_chimera_detection=False, reference_chimera_detection=False, cluster_size_filtering=False, remove_usearch_logs=True) # Chimera sequence should not be detected without reference test. expected_clusters = {'1': ['Solemya', 'Solemya_seq2'], '0': ['usearch_ecoli_seq', 'usearch_ecoli_seq2'], '2': ['chimera']} expected_failures = [] self.assertEqual(clusters, expected_clusters) self.assertEqual(failures, expected_failures) def test_usearch_qf_generates_logs(self): """ Generates expected log files """ curr_output_dir = get_tmp_filename(prefix='/UsearchLogTest_',suffix='/') create_dir(curr_output_dir) self._dirs_to_remove.append(curr_output_dir) # cluster size filtering set to 1 instead of default 4 clusters, failures = usearch_qf(self.tmp_seq_filepath2, output_dir = curr_output_dir, db_filepath = self.tmp_ref_database, minsize = 1, remove_usearch_logs=False, chimeras_retention = 'intersection') expected_clusters = {'1': ['Solemya', 'Solemya_seq2'], '0': ['usearch_ecoli_seq', 'usearch_ecoli_seq2']} expected_failures = ['chimera'] self.assertEqual(clusters, expected_clusters) self.assertEqual(failures, expected_failures) # Only checking for creation of files, as file contents contain # tmp file names. expected_log_names = ['assign_reads_to_otus.log', 'uchime_de_novo_chimera_filtering.log', 'derep.log', 'uchime_reference_chimera_filtering.log', 'minsize_0_abundance_sort.log', 'usearch_cluster_err_corrected.log', 'minsize_1_abundance_sort.log', 'usearch_cluster_seqs.log', 'sortlen.log'] actual_logs =\ [basename(curr_file) for curr_file in glob(curr_output_dir + "*.*")] for log in expected_log_names: self.assertContains(actual_logs, log) def test_concatenate_fastas(self): """ Properly concatenates two fasta files """ out_f =\ get_tmp_filename(prefix='UsearchConcatFileTest_',suffix='.fasta') actual_concatenated_seqs = concatenate_fastas(self.tmp_seq_filepath1, self.tmp_seq_filepath2, out_f) self._files_to_remove.append(out_f) actual_lines =\ [line.strip() for line in open(actual_concatenated_seqs, "U")] self.assertEqual(actual_lines, expected_combined_dna_seqs_1_seqs_usearch) def test_assign_reads_to_otus(self): """ Properly assigns reads back to original ID """ app_result, output_filepath =\ assign_reads_to_otus(original_fasta = self.tmp_ref_database, filtered_fasta = self.tmp_seq_filepath2, remove_usearch_logs = True, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) # Stripping off first line, which refers to the command using tmp # file names, retaining other actual results. actual_assignments =\ [line.strip() for line in open(output_filepath, "U")][2:] self.assertEqual(actual_assignments, self.expected_otu_assignments) def test_enumerate_otus(self): """ Enumerates OTUs properly """ output_filepath = enumerate_otus(self.tmp_seq_filepath1) self._files_to_remove.append(output_filepath) actual_fasta = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_fasta, self.expected_enumerated_fasta) def test_enumerate_otus_added_options(self): """ Enumerates with all options properly """ output_filepath = enumerate_otus(self.tmp_seq_filepath1, label_prefix = "Big", label_suffix = "Ern", retain_label_as_comment = True, count_start = 255) self._files_to_remove.append(output_filepath) actual_fasta = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_fasta, self.expected_enumerated_fasta_added_options) def test_usearch_cluster_seqs(self): """ Clusters sequences correctly """ # clusters all seqs with default 97% identity app_result, output_filepath =\ usearch_cluster_seqs(self.tmp_seqs_w_abundance, save_intermediate_files=False, remove_usearch_logs=True, percent_id = 0.97, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_clusters = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_clusters, self.expected_clusters_w_abundance_default_settings) def test_usearch_cluster_seqs_high_identity(self): """ Clusters sequences correctly """ # Should get two clusters with 99.9% identity app_result, output_filepath =\ usearch_cluster_seqs(self.tmp_seqs_w_abundance, save_intermediate_files=False, remove_usearch_logs=True, percent_id = 0.999, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_clusters = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_clusters, self.expected_clusters_w_abundance_low_setting) def test_usearch_chimera_filter_ref_based(self): """ Properly detects chimeras against reference database """ app_result, output_filepath =\ usearch_chimera_filter_ref_based(self.tmp_seq_filepath2, self.tmp_ref_database, remove_usearch_logs=True, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_filtered_chimeras =\ [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_filtered_chimeras, self.expected_reference_filtered_seqs) def test_usearch_chimera_filter_de_novo(self): """ Properly detects de novo chimeras """ app_result, output_filepath =\ usearch_chimera_filter_de_novo(self.tmp_de_novo_chimera_seqs, remove_usearch_logs=True, abundance_skew = 2, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_seqs = \ [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_seqs, self.expected_de_novo_chimeras_default) def test_usearch_chimera_filter_de_novo_abundance_skew(self): """ Properly detects de novo chimeras with skew changes """ app_result, output_filepath =\ usearch_chimera_filter_de_novo(self.tmp_de_novo_chimera_seqs, remove_usearch_logs=True, abundance_skew = 11, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_seqs = \ [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_seqs, self.expected_de_novo_chimera_filtered_skew11) def test_usearch_cluster_error_correction(self): """ Properly clusters seqs for chimera testing/filtering """ # clusters all seqs with default 97% identity app_result, output_filepath =\ usearch_cluster_error_correction(self.tmp_seqs_w_abundance, save_intermediate_files=False, remove_usearch_logs=True, percent_id_err = 0.97, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_clusters = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_clusters, self.expected_cluster_err_seqs) def test_usearch_sort_by_abundance(self): """ Properly sorts fasta by abundance """ app_result, output_filepath =\ usearch_sort_by_abundance(self.tmp_de_novo_chimera_seqs, remove_usearch_logs=True, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_seqs = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_seqs, self.expected_sorted_by_abundance_no_filter) def test_usearch_sort_by_abundance_filter(self): """ Properly sorts fasta by abundance, filters low count otus """ app_result, output_filepath =\ usearch_sort_by_abundance(self.tmp_de_novo_chimera_seqs, remove_usearch_logs=True, minsize = 40, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_seqs = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_seqs, self.expected_abundance_sort_filtered) def test_usearch_dereplicate_exact_subseqs(self): """ Properly dereplicates fasta file """ app_result, output_filepath =\ usearch_dereplicate_exact_subseqs(self.tmp_dna_seqs_with_dups, remove_usearch_logs=True, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_seqs = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_seqs, self.expected_derep_seqs) def test_usearch_dereplicate_exact_seqs(self): """ Properly dereplicates fasta file """ app_result, output_filepath =\ usearch_dereplicate_exact_seqs(self.tmp_dna_seqs_with_dups, remove_usearch_logs=True, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_seqs = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_seqs, self.expected_derep_seqs_full_len) def test_usearch_fasta_sort_from_filepath(self): """ Properly sorts fasta according to seq length """ app_result, output_filepath =\ usearch_fasta_sort_from_filepath(self.tmp_seq_filepath2, remove_usearch_logs=True, working_dir=self.tmp_dir) self._files_to_remove.append(output_filepath) actual_seqs = [line.strip() for line in open(output_filepath, "U")] self.assertEqual(actual_seqs, self.expected_len_sorted_seqs) def test_clusters_from_blast_uc_file(self): """ clusters_from_uc_file functions as expected """ expected_clusters = {'19': ['PC.634_4'], '42': ['PC.test2_1', 'PC.test1_2', 'PC.634_3'], '6': ['PC.269_5']} expected_failures = ['PC.481_6'] self.assertEqual(clusters_from_blast_uc_file(self.uc_lines1), (expected_clusters,expected_failures)) def test_get_retained_chimeras_union(self): """ Properly returns union of two fastas """ out_f =\ get_tmp_filename(prefix='UsearchUnionTest_',suffix='.fasta') actual_out_fp = get_retained_chimeras(self.tmp_retained_chimeras_seqs1, self.tmp_retained_chimeras_seqs2, out_f, chimeras_retention = 'union') self._files_to_remove.append(out_f) actual_out_f = [line.strip() for line in open(actual_out_fp, "U")] self.assertEqual(actual_out_f, self.expected_retained_chimeras_union) def test_get_retained_chimeras_intersection(self): """ Properly returns intersection of two fastas """ out_f =\ get_tmp_filename(prefix='UsearchIntersectionTest_',suffix='.fasta') actual_out_fp = get_retained_chimeras(self.tmp_retained_chimeras_seqs1, self.tmp_retained_chimeras_seqs2, out_f, chimeras_retention = 'intersection') self._files_to_remove.append(out_f) actual_out_f = [line.strip() for line in open(actual_out_fp, "U")] self.assertEqual(actual_out_f, self.expected_retained_chimeras_intersection) def test_assign_dna_reads_to_protein_database(self): """assign_dna_reads_to_protein_database wrapper functions as expected """ output_dir = get_random_directory_name(output_dir=self.tmp_dir) self._dirs_to_remove.append(output_dir) output_fp = join(output_dir,'out.uc') assign_dna_reads_to_protein_database(self.dna_seqs3_filepath, self.protein_ref_seqs1_filepath, output_fp, temp_dir = self.tmp_dir) self.assertTrue(exists(output_fp)) self.assertTrue(exists(output_fp.replace('.uc','.bl6'))) # confirm that the clusters look like what we expect expected_clusters = [['eco:b0015'],['eco:b0122','eco:b0122-like']] expected_clusters.sort() actual_clusters = clusters_from_blast_uc_file(open(output_fp))[0].values() actual_clusters.sort() self.assertEqual(actual_clusters,expected_clusters) def test_assign_dna_reads_to_protein_database_alt_params(self): """assign_dna_reads_to_protein_database wrapper functions with alt params """ output_dir = get_random_directory_name(output_dir=self.tmp_dir) self._dirs_to_remove.append(output_dir) output_fp = join(output_dir,'out.uc') assign_dna_reads_to_protein_database(self.dna_seqs3_filepath, self.protein_ref_seqs1_filepath, output_fp, temp_dir = self.tmp_dir, params={'--id':1.0}) self.assertTrue(exists(output_fp)) self.assertTrue(exists(output_fp.replace('.uc','.bl6'))) # confirm that the clusters look like what we expect expected_clusters = [['eco:b0015'],['eco:b0122']] expected_clusters.sort() actual_clusters = clusters_from_blast_uc_file(open(output_fp))[0].values() actual_clusters.sort() self.assertEqual(actual_clusters,expected_clusters) def test_assign_dna_reads_to_dna_database(self): """assign_dna_reads_to_protein_database wrapper functions as expected """ output_dir = get_random_directory_name(output_dir=self.tmp_dir) self._dirs_to_remove.append(output_dir) output_fp = join(output_dir,'out.uc') assign_dna_reads_to_protein_database(self.dna_seqs3_filepath, self.dna_seqs4_filepath, output_fp, temp_dir = self.tmp_dir) self.assertTrue(exists(output_fp)) self.assertTrue(exists(output_fp.replace('.uc','.bl6'))) # confirm that the clusters look like what we expect expected_clusters = [['eco:b0015'],['eco:b0122','eco:b0122-like']] expected_clusters.sort() actual_clusters = clusters_from_blast_uc_file(open(output_fp))[0].values() actual_clusters.sort() self.assertEqual(actual_clusters,expected_clusters) # Long strings for test files, output, etc. # ************************************************* retained_chimeras_seqs1 = """>seq1 ACAGGCC >seq2 ACAGGCCCCC >seq3 TTATCCATT""" retained_chimeras_seqs2 = """>seq3 ACAGGCC >seq4 ACAGGCCCCC >seq5 TTATCCATT""" dna_seqs_1 = """>uclust_test_seqs_0 some comment0 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >uclust_test_seqs_1 some comment1 ACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT >uclust_test_seqs_2 some comment2 CCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT >uclust_test_seqs_3 some comment3 CCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT >uclust_test_seqs_4 some comment4 GCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT >uclust_test_seqs_5 some comment4_again CCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA >uclust_test_seqs_6 some comment6 CGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT >uclust_test_seqs_7 some comment7 ACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT >uclust_test_seqs_8 some comment8 CGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT >uclust_test_seqs_9 some comment9 GGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA""" dna_seqs_3 = """>eco:b0001 thrL; thr operon leader peptide; K08278 thr operon leader peptide (N) atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg ggctga >eco:b0015 dnaJ; chaperone Hsp40, co-chaperone with DnaK; K03686 molecular chaperone DnaJ (N) atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa >eco:b0122 yacC; conserved protein, PulS_OutS family (N) atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaataa >eco:b0122-like atgaagaaaattttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaatcc""" dna_seqs_4 = """>eco:b0015 dnaJ; chaperone Hsp40, co-chaperone with DnaK; K03686 molecular chaperone DnaJ (N) atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa >eco:b0122 yacC; conserved protein, PulS_OutS family (N) atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaataa >eco:b0122-like atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaatcc""" protein_ref_seqs1 = """>eco:b0001 thrL; thr operon leader peptide; K08278 thr operon leader peptide (A) MKRISTTITTTITITTGNGAG >eco:b0015 dnaJ; chaperone Hsp40, co-chaperone with DnaK; K03686 molecular chaperone DnaJ (A) MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDS QKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYN MELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQ QTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPAGVDTGDRIRLAGEGEAGEHGAP AGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEIEVPTLDGRVKLKVPGETQTG KLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGGPTGEHNSPRS KSFFDGVKKFFDDLTR >eco:b0015:rep MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDS QKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYN MELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQ QTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPAGVDTGDRIRLAGEGEAGEHGAP AGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEIEVPTLDGRVKLKVPGETQTG KLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGGPTGEHNSPRS KSFFDGVKKFFDDLTR >eco:b0122 yacC; conserved protein, PulS_OutS family (A) MKTFFRTVLFGSLMAVCANSYALSESEAEDMADLTAVFVFLKNDCGYQNLPNGQIRRALV FFAQQNQWDLSNYDTFDMKALGEDSYRDLSGIGIPVAKKCKALARDSLSLLAYVK""" usearch_ref_seqs1 = """>ref1 ecoli sequence CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCA >EU199232 1 1236 Bacteria/Deltaproteobacteria/Desulfurella - Hippea/uncultured TACGCGCGGAAATCGAGCGAGATTGGGAACGCAAGTTCCTGAGTATTGCGGCGAACGGGTGAGTAAGACGTGGGTGATCTACCCCTAGGGTGGGAATAACCCGGGGAAACCCGGGCTAATACCGAATAAGACCACAGGAGGCGACTCCAGAGGGTCAAAGGGAGCCTTGGCCTCCCCC >L07864 1 1200 Bacteria/Beta Gammaproteobacteria/Solemya symbiont GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTAATGCATGGGAATCTGCCATATAGTGGGGGACAACTGGGGAAACCCAGGCTAATACCGCATAATCTCTACGGAGGAAAGGCTTC """ dna_seqs_usearch = """>usearch_ecoli_seq CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGT >Solemya seq GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTA >usearch_ecoli_seq2 CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTCCAT >Solemya_seq2 GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTATCAAG >chimera CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACCCCTAGGGTGGGAATAACCCGGGGAAACCCGGGCTAATACCGAATAAGACCACAGGAGGCGACTCCAGAGGGTCAAAGGGAGCCTTGGCCTCCCCC """ dna_seqs_reference_otu_picking = """>usearch_ecoli_seq CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGT >Solemya seq GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTA >usearch_ecoli_seq2 CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTCCAT >Solemya_seq2 GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTATCAAG >RandomCrap ACACAAACAGTATATTATATCCCCAGACAGGGACCGAGATTTACCACACCCAAAAAAAAAAAAAACACACCCCCCCCCCCCCCACACACACACTTATTTT """ dna_seqs_with_abundance = """>Cluster1;size=114 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >Cluster2;size=45 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCC >Cluster0;size=37 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGAACATCGCGTCAGGTTTGTGTCAGGCCT >Cluster7;size=33 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAAGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >Cluster6;size=32 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >Cluster5;size=25 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >Cluster11;size=22 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >Cluster12;size=15 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >Cluster13;size=2 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTGTGTCAGGCCT >Cluster14;size=1 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTG""" de_novo_chimera_seqs = """>Cluster1;size=52 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACAC CGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGT TATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster0;size=50 TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCC CGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCA TCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCGG >Cluster2;size=45 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCC CGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTT >Cluster10;size=43 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCC CGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTC CTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCG >Cluster4;size=40 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGTCCCATGCAGGACCGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG >Cluster6;size=40 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTA CGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGG >Cluster3;size=30 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTCAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCT TACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTG TTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG >Cluster12;size=19 TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTGGTCTTGGTGAGCCGTTACCC CACCAACTAACTAATACAACGCATGCCCATCCATTACCACCGGAGTTTTCAACCCAAGAAGATGCCTCCCTGGATGTTAT GGGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTAATGGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTC GCCGACAAT >Cluster30;size=18 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCC CGCCAACTAGCTAATGCGCCGCATGGCCATCCGTAGCCGGTGTTACCCTTTAAACCCCAAGAGATGCCTCTCGGAGTTAT TACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTACGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster29;size=18 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGCCCATCCGCCACCGGTAATCCCTTTGGCGGCACCGGGATGCCCCGACGCCGCGTC ACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTGGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGG TCGCCGG >Cluster16;size=16 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCC CTCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTA TGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGGCAGGTTACCCACGCGTTACTCACCCGTCCGCCACT >Cluster222;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTAT GCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACT >Cluster221;size=1 CTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTAGGCCGTTGCCC CGCCAACTACCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATTATCTCACCATGCGGCAAAATAATGT CATGCGGTATTAGCGTTCGTTTCCAAACGTTATCCCCCTCTGAAAGGCAGGTTGCTCACGCGTT >Cluster218;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGCCACCCTCTCAGGTCGGCTACTGATCGTCACCTTGGTAGGCCGTTACCC CACCAACTAGCTAATCAGACGCAAGCCCATCTATCAGCGGATTGCTCCTTTTCTAGCTATATCATGCGATACTACTAGCT TATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCTGATAGGCAGG >Cluster217;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGAGTCCATCTCAGAGCGATAAATCTTTGATATCCAGAGCCATGCGACCCAGATATATT ATGCGGTATTAGCAGCTGTTTCCAGCTGTTATTCCCCATCCAAGGCAGGTT >Cluster216;size=1 CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGTCAGCTACTGATCGTCGCCTTGGTAGGCCATTACCC TACCAACTAGCTAATCAGACGCGAGGCCATCTCTCAGCGATAAATCTTTGATATATCTGCCATGCGACAAACATATATTA TGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTT >Cluster522;size=10 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTAT GCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACT""" dna_seqs_with_dups=""">seq1 GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTAA >seq2 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC >seq3 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC >seq4 GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTT""" # Expected output file data uc_lines1 = """# usearch --id 0.97 --uc usearch_picked_otus/assign_reads_to_otus.uc --query seqs.fna --global --db usearch_picked_otus/enumerated_otus.fasta # version=4.2.66 # Tab-separated fields: # 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel # Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit # For C and D types, PctId is average id with seed. # QueryStart and SeedStart are zero-based relative to start of sequence. # If minus strand, SeedStart is relative to reverse-complemented seed. H\t42\t217\t99.1\t+\t0\t0\t217MI\tPC.test2_1 FLP3FBN02xELBSXx orig_bc=ACAGAGTCGGCG new_bc=ACAGAGTCGGCG,FLP3FBN02x bc_diffs=0\t42 H\t42\t217\t99.1\t+\t0\t0\t217MI\tPC.test1_2 FLP3FBN03ELBSXx orig_bc=ACAGAGTCGGCG new_bc=ACAGAGTCGGCG,FLP3FBN03 bc_diffs=0\t42 H\t42\t217\t99.1\t+\t0\t0\t217MI\tPC.634_3 FLP3FBN01ELBSX orig_bc=TCAGAGTCGGCT new_bc=ACAGAGTCGGCT,FLP3FBN01 bc_diffs=1\t42 H\t19\t243\t100.0\t+\t0\t0\t25MI218M\tPC.634_4 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT,FLP3FBN01 bc_diffs=0\t19 N\t*\t219\t*\t*\t*\t*\t*\tPC.481_6\tFLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG,FLP3FBN01 bc_diffs=0\t* H\t6\t211\t99.5\t+\t0\t0\t211M\tPC.269_5 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA,FLP3FBN01 bc_diffs=0\t6 """.split('\n') expected_otu_assignments = """# Tab-separated fields: # 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel # Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit # For C and D types, PctId is average id with seed. # QueryStart and SeedStart are zero-based relative to start of sequence. # If minus strand, SeedStart is relative to reverse-complemented seed. H\t2\t199\t97.5\t.\t0\t0\t119M80D\tref1 ecoli sequence\tusearch_ecoli_seq2 N\t*\t178\t*\t*\t*\t*\t*\tEU199232 1 1236 Bacteria/Deltaproteobacteria/Desulfurella - Hippea/uncultured\t* H\t1\t180\t100.0\t.\t0\t0\t97M83D\tL07864 1 1200 Bacteria/Beta Gammaproteobacteria/Solemya symbiont\tSolemya seq""".split('\n') expected_enumerated_fasta = """>0 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >1 ACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT >2 CCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT >3 CCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT >4 GCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT >5 CCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA >6 CGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT >7 ACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT >8 CGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT >9 GGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA""".split('\n') expected_enumerated_fasta_added_options = """>Big255Ern\tuclust_test_seqs_0 some comment0 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >Big256Ern\tuclust_test_seqs_1 some comment1 ACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT >Big257Ern\tuclust_test_seqs_2 some comment2 CCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT >Big258Ern\tuclust_test_seqs_3 some comment3 CCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT >Big259Ern\tuclust_test_seqs_4 some comment4 GCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT >Big260Ern\tuclust_test_seqs_5 some comment4_again CCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA >Big261Ern\tuclust_test_seqs_6 some comment6 CGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT >Big262Ern\tuclust_test_seqs_7 some comment7 ACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT >Big263Ern\tuclust_test_seqs_8 some comment8 CGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT >Big264Ern\tuclust_test_seqs_9 some comment9 GGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA""".split('\n') expected_clusters_w_abundance_default_settings = """>Cluster1;size=326 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT""".split('\n') expected_clusters_w_abundance_low_setting = """>Cluster1;size=304 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >Cluster11;size=22 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCTAACCC CCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT""".split('\n') expected_reference_filtered_seqs = """>usearch_ecoli_seq CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTG ACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGT >Solemya seq GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAG TGGCGGACGGGTGAGTA >usearch_ecoli_seq2 CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTG ACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTCCAT >Solemya_seq2 GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAG TGGCGGACGGGTGAGTATCAAG""".split('\n') expected_de_novo_chimeras_default = """>Cluster1;size=52 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACAC CGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGT TATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster0;size=50 TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCC CGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCA TCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCGG >Cluster2;size=45 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCC CGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTT >Cluster10;size=43 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCC CGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTC CTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCG >Cluster4;size=40 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGTCCCATGCAGGACCGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG >Cluster6;size=40 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTA CGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGG >Cluster3;size=30 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTCAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCT TACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTG TTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG >Cluster12;size=19 TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTGGTCTTGGTGAGCCGTTACCC CACCAACTAACTAATACAACGCATGCCCATCCATTACCACCGGAGTTTTCAACCCAAGAAGATGCCTCCCTGGATGTTAT GGGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTAATGGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTC GCCGACAAT >Cluster29;size=18 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGCCCATCCGCCACCGGTAATCCCTTTGGCGGCACCGGGATGCCCCGACGCCGCGTC ACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTGGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGG TCGCCGG >Cluster30;size=18 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCC CGCCAACTAGCTAATGCGCCGCATGGCCATCCGTAGCCGGTGTTACCCTTTAAACCCCAAGAGATGCCTCTCGGAGTTAT TACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTACGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster16;size=16 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCC CTCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTA TGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGGCAGGTTACCCACGCGTTACTCACCCGTCCGCCACT >Cluster221;size=1 CTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTAGGCCGTTGCCC CGCCAACTACCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATTATCTCACCATGCGGCAAAATAATGT CATGCGGTATTAGCGTTCGTTTCCAAACGTTATCCCCCTCTGAAAGGCAGGTTGCTCACGCGTT >Cluster218;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGCCACCCTCTCAGGTCGGCTACTGATCGTCACCTTGGTAGGCCGTTACCC CACCAACTAGCTAATCAGACGCAAGCCCATCTATCAGCGGATTGCTCCTTTTCTAGCTATATCATGCGATACTACTAGCT TATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCTGATAGGCAGG >Cluster217;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGAGTCCATCTCAGAGCGATAAATCTTTGATATCCAGAGCCATGCGACCCAGATATATT ATGCGGTATTAGCAGCTGTTTCCAGCTGTTATTCCCCATCCAAGGCAGGTT >Cluster216;size=1 CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGTCAGCTACTGATCGTCGCCTTGGTAGGCCATTACCC TACCAACTAGCTAATCAGACGCGAGGCCATCTCTCAGCGATAAATCTTTGATATATCTGCCATGCGACAAACATATATTA TGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTT""".split('\n') expected_de_novo_chimera_filtered_skew11 = """>Cluster1;size=52 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACAC CGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGT TATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster0;size=50 TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCC CGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCA TCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCGG >Cluster2;size=45 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCC CGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTT >Cluster10;size=43 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCC CGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTC CTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCG >Cluster4;size=40 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGTCCCATGCAGGACCGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG >Cluster6;size=40 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTA CGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGG >Cluster3;size=30 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTCAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCT TACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTG TTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG >Cluster12;size=19 TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTGGTCTTGGTGAGCCGTTACCC CACCAACTAACTAATACAACGCATGCCCATCCATTACCACCGGAGTTTTCAACCCAAGAAGATGCCTCCCTGGATGTTAT GGGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTAATGGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTC GCCGACAAT >Cluster29;size=18 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGCCCATCCGCCACCGGTAATCCCTTTGGCGGCACCGGGATGCCCCGACGCCGCGTC ACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTGGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGG TCGCCGG >Cluster30;size=18 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCC CGCCAACTAGCTAATGCGCCGCATGGCCATCCGTAGCCGGTGTTACCCTTTAAACCCCAAGAGATGCCTCTCGGAGTTAT TACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTACGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster16;size=16 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCC CTCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTA TGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGGCAGGTTACCCACGCGTTACTCACCCGTCCGCCACT >Cluster522;size=10 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTAT GCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACT >Cluster221;size=1 CTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTAGGCCGTTGCCC CGCCAACTACCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATTATCTCACCATGCGGCAAAATAATGT CATGCGGTATTAGCGTTCGTTTCCAAACGTTATCCCCCTCTGAAAGGCAGGTTGCTCACGCGTT >Cluster218;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGCCACCCTCTCAGGTCGGCTACTGATCGTCACCTTGGTAGGCCGTTACCC CACCAACTAGCTAATCAGACGCAAGCCCATCTATCAGCGGATTGCTCCTTTTCTAGCTATATCATGCGATACTACTAGCT TATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCTGATAGGCAGG >Cluster217;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGAGTCCATCTCAGAGCGATAAATCTTTGATATCCAGAGCCATGCGACCCAGATATATT ATGCGGTATTAGCAGCTGTTTCCAGCTGTTATTCCCCATCCAAGGCAGGTT >Cluster216;size=1 CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGTCAGCTACTGATCGTCGCCTTGGTAGGCCATTACCC TACCAACTAGCTAATCAGACGCGAGGCCATCTCTCAGCGATAAATCTTTGATATATCTGCCATGCGACAAACATATATTA TGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTT""".split('\n') expected_cluster_err_seqs = """>Cluster0;size=2 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT""".split('\n') expected_sorted_by_abundance_no_filter = """>Cluster1;size=52 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACAC CGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGT TATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster0;size=50 TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCC CGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCA TCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCGG >Cluster2;size=45 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCC CGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTT >Cluster10;size=43 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCC CGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTC CTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCG >Cluster4;size=40 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGTCCCATGCAGGACCGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG >Cluster6;size=40 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTA CGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGG >Cluster3;size=30 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTCAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCT TACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTG TTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG >Cluster12;size=19 TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTGGTCTTGGTGAGCCGTTACCC CACCAACTAACTAATACAACGCATGCCCATCCATTACCACCGGAGTTTTCAACCCAAGAAGATGCCTCCCTGGATGTTAT GGGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTAATGGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTC GCCGACAAT >Cluster29;size=18 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGCCCATCCGCCACCGGTAATCCCTTTGGCGGCACCGGGATGCCCCGACGCCGCGTC ACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTGGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGG TCGCCGG >Cluster30;size=18 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCC CGCCAACTAGCTAATGCGCCGCATGGCCATCCGTAGCCGGTGTTACCCTTTAAACCCCAAGAGATGCCTCTCGGAGTTAT TACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTACGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster16;size=16 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCC CTCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTA TGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGGCAGGTTACCCACGCGTTACTCACCCGTCCGCCACT >Cluster522;size=10 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTAT GCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACT >Cluster222;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTAT GCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACT >Cluster221;size=1 CTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTAGGCCGTTGCCC CGCCAACTACCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATTATCTCACCATGCGGCAAAATAATGT CATGCGGTATTAGCGTTCGTTTCCAAACGTTATCCCCCTCTGAAAGGCAGGTTGCTCACGCGTT >Cluster218;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGCCACCCTCTCAGGTCGGCTACTGATCGTCACCTTGGTAGGCCGTTACCC CACCAACTAGCTAATCAGACGCAAGCCCATCTATCAGCGGATTGCTCCTTTTCTAGCTATATCATGCGATACTACTAGCT TATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCTGATAGGCAGG >Cluster217;size=1 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGAGTCCATCTCAGAGCGATAAATCTTTGATATCCAGAGCCATGCGACCCAGATATATT ATGCGGTATTAGCAGCTGTTTCCAGCTGTTATTCCCCATCCAAGGCAGGTT >Cluster216;size=1 CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGTCAGCTACTGATCGTCGCCTTGGTAGGCCATTACCC TACCAACTAGCTAATCAGACGCGAGGCCATCTCTCAGCGATAAATCTTTGATATATCTGCCATGCGACAAACATATATTA TGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTT""".split('\n') expected_abundance_sort_filtered = """>Cluster1;size=52 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACAC CGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGT TATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCG GTCGCCGG >Cluster0;size=50 TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCC CGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCA TCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCGG >Cluster2;size=45 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCC CGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTT >Cluster10;size=43 CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCC CGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTC CTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCG >Cluster4;size=40 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCC CGCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGTCCCATGCAGGACCGTGCGCTTA TGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG >Cluster6;size=40 CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCC CGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTA CGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGG""".split('\n') expected_derep_seqs = """>seq1;size=2 GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTAA >seq2;size=2 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC""".split('\n') expected_derep_seqs_full_len = """>Cluster0;size=1 GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTAA >Cluster1;size=2 TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCC >Cluster2;size=1 GCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTT""".split('\n') expected_len_sorted_seqs = """>chimera CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACCCCTAGGGTGGGAATAACCCGGGGAAACCCGGGCTAATACCGAATAAGACCACAGGAGGCGACTCCAGAGGGTCAAAGGGAGCCTTGGCCTCCCCC >usearch_ecoli_seq2 CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTCCAT >usearch_ecoli_seq CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGT >Solemya_seq2 GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTATCAAG >Solemya seq GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTA""".split('\n') expected_combined_dna_seqs_1_seqs_usearch = """>uclust_test_seqs_0 some comment0 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT >uclust_test_seqs_1 some comment1 ACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT >uclust_test_seqs_2 some comment2 CCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT >uclust_test_seqs_3 some comment3 CCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT >uclust_test_seqs_4 some comment4 GCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT >uclust_test_seqs_5 some comment4_again CCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA >uclust_test_seqs_6 some comment6 CGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT >uclust_test_seqs_7 some comment7 ACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT >uclust_test_seqs_8 some comment8 CGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT >uclust_test_seqs_9 some comment9 GGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA >usearch_ecoli_seq CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGT >Solemya seq GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTA >usearch_ecoli_seq2 CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTCCAT >Solemya_seq2 GGCTCAGATTGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGGTAACAGGCGGAGCTTGCTCTGCGCTGACGAGTGGCGGACGGGTGAGTATCAAG >chimera CGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAGGGAGTAAAGTTAATACCTTTGCTCATTGACCCCTAGGGTGGGAATAACCCGGGGAAACCCGGGCTAATACCGAATAAGACCACAGGAGGCGACTCCAGAGGGTCAAAGGGAGCCTTGGCCTCCCCC""".split('\n') expected_retained_chimeras_union = """>seq1 ACAGGCC >seq2 ACAGGCCCCC >seq3 TTATCCATT >seq4 ACAGGCCCCC >seq5 TTATCCATT""".split('\n') expected_retained_chimeras_intersection = """>seq3 TTATCCATT""".split('\n') if __name__ == '__main__': main()