def load_tree_files(tree_dir): """Load trees from filepaths checks if filenames indicate that trees are from different distance methods. If so, warns user. loads trees into phylonode objects returns [trees] raises a RuntimeError if no trees are loaded """ tree_file_names = os.listdir(tree_dir) # ignore invisible files like .DS_Store tree_file_names = [ fname for fname in tree_file_names if not fname.startswith('.') ] # try to warn user if using multiple types of trees { try: base_names = [] for fname in tree_file_names: base_names.append(parse_rarefaction_fname(fname)[0]) except ValueError: pass else: if len(set(base_names)) > 1: warnstr = """ warning: trees are named differently, please be sure you're not comparing trees generated in different manners, unless you're quite sure that's what you intend to do. types: """ + str(set(base_names)) + """ continuing anyway...""" warn(warnstr) # } trees = [] for fname in tree_file_names: try: f = open(os.path.join(tree_dir, fname), 'U') tree = TreeNode.from_newick(f) tree.filepath = fname trees.append(tree) f.close() except IOError as err: sys.stderr.write('error loading tree ' + fname + '\n') exit(1) if len(trees) == 0: raise RuntimeError('Error: no trees loaded' + ', check that tree directory has has valid trees') return trees
def load_tree_files(tree_dir): """Load trees from filepaths checks if filenames indicate that trees are from different distance methods. If so, warns user. loads trees into phylonode objects returns [trees] raises a RuntimeError if no trees are loaded """ tree_file_names = os.listdir(tree_dir) # ignore invisible files like .DS_Store tree_file_names = [fname for fname in tree_file_names if not fname.startswith('.')] # try to warn user if using multiple types of trees { try: base_names = [] for fname in tree_file_names: base_names.append(parse_rarefaction_fname(fname)[0]) except ValueError: pass else: if len(set(base_names)) > 1: warnstr = """ warning: trees are named differently, please be sure you're not comparing trees generated in different manners, unless you're quite sure that's what you intend to do. types: """ + str(set(base_names)) + """ continuing anyway...""" warn(warnstr) # } trees = [] for fname in tree_file_names: try: f = open(os.path.join(tree_dir, fname), 'U') tree = TreeNode.from_newick(f) tree.filepath = fname trees.append(tree) f.close() except IOError as err: sys.stderr.write('error loading tree ' + fname + '\n') exit(1) if len(trees) == 0: raise RuntimeError('Error: no trees loaded' + ', check that tree directory has has valid trees') return trees
def test_run_pick_de_novo_otus_muscle(self): """run_pick_de_novo_otus w muscle generates expected results """ self.params['assign_taxonomy'] = \ {'id_to_taxonomy_fp': self.test_data['refseqs_tax'][0], 'reference_seqs_fp': self.test_data['refseqs'][0]} self.params['align_seqs'] = {'alignment_method': 'muscle'} self.params['filter_alignment'] = \ {'suppress_lane_mask_filter': None, 'entropy_threshold': '0.10'} run_pick_de_novo_otus(self.test_data['seqs'][0], self.test_out, call_commands_serially, self.params, self.qiime_config, parallel=False, status_update_callback=no_status_updates) input_file_basename = splitext(split(self.test_data['seqs'][0])[1])[0] otu_map_fp = join(self.test_out, 'uclust_picked_otus', '%s_otus.txt' % input_file_basename) alignment_fp = join(self.test_out, 'muscle_aligned_seqs', '%s_rep_set_aligned.fasta' % input_file_basename) taxonomy_assignments_fp = join( self.test_out, 'uclust_assigned_taxonomy', '%s_rep_set_tax_assignments.txt' % input_file_basename) otu_table_fp = join(self.test_out, 'otu_table.biom') tree_fp = join(self.test_out, 'rep_set.tre') # Number of OTUs falls within a range that was manually # confirmed otu_map_lines = list(open(otu_map_fp)) num_otus = len(otu_map_lines) otu_map_otu_ids = [o.split()[0] for o in otu_map_lines] self.assertEqual(num_otus, 14) # all otus get taxonomy assignments taxonomy_assignment_lines = list(open(taxonomy_assignments_fp)) self.assertEqual(len(taxonomy_assignment_lines), num_otus) # all OTUs align self.assertEqual(count_seqs(alignment_fp)[0], num_otus) # all OTUs in tree with open(tree_fp) as f: tree = TreeNode.from_newick(f) self.assertEqual(len(list(tree.tips())), num_otus) # check that the two final output files have non-zero size self.assertTrue(getsize(tree_fp) > 0) self.assertTrue(getsize(otu_table_fp) > 0) # Check that the log file is created and has size > 0 log_fp = glob(join(self.test_out, 'log*.txt'))[0] self.assertTrue(getsize(log_fp) > 0) # parse the otu table otu_table = load_table(otu_table_fp) expected_sample_ids = [ 'f1', 'f2', 'f3', 'f4', 'p1', 'p2', 't1', 't2', 'not16S.1' ] # sample IDs are as expected self.assertItemsEqual(otu_table.ids(), expected_sample_ids) # expected OTUs self.assertItemsEqual(otu_table.ids(axis='observation'), otu_map_otu_ids) # number of sequences in the full otu table equals the number of # input sequences number_seqs_in_otu_table = sum( [v.sum() for v in otu_table.iter_data()]) self.assertEqual(number_seqs_in_otu_table, count_seqs(self.test_data['seqs'][0])[0])
def test_run_pick_de_novo_otus_parallel(self): """run_pick_de_novo_otus generates expected results in parallel """ self.params['assign_taxonomy'] = \ {'id_to_taxonomy_fp': self.test_data['refseqs_tax'][0], 'reference_seqs_fp': self.test_data['refseqs'][0]} self.params['align_seqs'] = \ {'template_fp': self.test_data['refseqs_aligned'][0]} self.params['filter_alignment'] = \ {'lane_mask_fp': self.test_data['refseqs_aligned_lanemask'][0]} actual_tree_fp, actual_otu_table_fp = run_pick_de_novo_otus( self.test_data['seqs'][0], self.test_out, call_commands_serially, self.params, self.qiime_config, parallel=True, status_update_callback=no_status_updates) input_file_basename = splitext(split(self.test_data['seqs'][0])[1])[0] otu_map_fp = join(self.test_out, 'uclust_picked_otus', '%s_otus.txt' % input_file_basename) alignment_fp = join(self.test_out, 'pynast_aligned_seqs', '%s_rep_set_aligned.fasta' % input_file_basename) failures_fp = join(self.test_out, 'pynast_aligned_seqs', '%s_rep_set_failures.fasta' % input_file_basename) taxonomy_assignments_fp = join( self.test_out, 'uclust_assigned_taxonomy', '%s_rep_set_tax_assignments.txt' % input_file_basename) otu_table_fp = join(self.test_out, 'otu_table.biom') tree_fp = join(self.test_out, 'rep_set.tre') self.assertEqual(actual_tree_fp, tree_fp) self.assertEqual(actual_otu_table_fp, otu_table_fp) # Number of OTUs falls within a range that was manually # confirmed otu_map_lines = list(open(otu_map_fp)) num_otus = len(otu_map_lines) otu_map_otu_ids = [o.split()[0] for o in otu_map_lines] self.assertEqual(num_otus, 14) # all otus get taxonomy assignments taxonomy_assignment_lines = list(open(taxonomy_assignments_fp)) self.assertEqual(len(taxonomy_assignment_lines), num_otus) # number of seqs which aligned + num of seqs which failed to # align sum to the number of OTUs self.assertEqual( count_seqs(alignment_fp)[0] + count_seqs(failures_fp)[0], num_otus) # number of tips in the tree equals the number of sequences that # aligned with open(tree_fp) as f: tree = TreeNode.from_newick(f) self.assertEqual(len(list(tree.tips())), count_seqs(alignment_fp)[0]) # parse the otu table otu_table = load_table(otu_table_fp) expected_sample_ids = [ 'f1', 'f2', 'f3', 'f4', 'p1', 'p2', 't1', 't2', 'not16S.1' ] # sample IDs are as expected self.assertItemsEqual(otu_table.ids(), expected_sample_ids) # otu ids are as expected self.assertItemsEqual(otu_table.ids(axis='observation'), otu_map_otu_ids) # number of sequences in the full otu table equals the number of # input sequences number_seqs_in_otu_table = sum( [v.sum() for v in otu_table.iter_data()]) self.assertEqual(number_seqs_in_otu_table, count_seqs(self.test_data['seqs'][0])[0]) # Check that the log file is created and has size > 0 log_fp = glob(join(self.test_out, 'log*.txt'))[0] self.assertTrue(getsize(log_fp) > 0)
def test_run_pick_de_novo_otus_muscle(self): """run_pick_de_novo_otus w muscle generates expected results """ self.params['assign_taxonomy'] = \ {'id_to_taxonomy_fp': self.test_data['refseqs_tax'][0], 'reference_seqs_fp': self.test_data['refseqs'][0]} self.params['align_seqs'] = {'alignment_method': 'muscle'} self.params['filter_alignment'] = \ {'suppress_lane_mask_filter': None, 'entropy_threshold': '0.10'} run_pick_de_novo_otus( self.test_data['seqs'][0], self.test_out, call_commands_serially, self.params, self.qiime_config, parallel=False, status_update_callback=no_status_updates) input_file_basename = splitext(split(self.test_data['seqs'][0])[1])[0] otu_map_fp = join(self.test_out, 'uclust_picked_otus', '%s_otus.txt' % input_file_basename) alignment_fp = join(self.test_out, 'muscle_aligned_seqs', '%s_rep_set_aligned.fasta' % input_file_basename) taxonomy_assignments_fp = join(self.test_out, 'uclust_assigned_taxonomy', '%s_rep_set_tax_assignments.txt' % input_file_basename) otu_table_fp = join(self.test_out, 'otu_table.biom') tree_fp = join(self.test_out, 'rep_set.tre') # Number of OTUs falls within a range that was manually # confirmed otu_map_lines = list(open(otu_map_fp)) num_otus = len(otu_map_lines) otu_map_otu_ids = [o.split()[0] for o in otu_map_lines] self.assertEqual(num_otus, 14) # all otus get taxonomy assignments taxonomy_assignment_lines = list(open(taxonomy_assignments_fp)) self.assertEqual(len(taxonomy_assignment_lines), num_otus) # all OTUs align self.assertEqual(count_seqs(alignment_fp)[0], num_otus) # all OTUs in tree with open(tree_fp) as f: tree = TreeNode.from_newick(f) self.assertEqual(len(list(tree.tips())), num_otus) # check that the two final output files have non-zero size self.assertTrue(getsize(tree_fp) > 0) self.assertTrue(getsize(otu_table_fp) > 0) # Check that the log file is created and has size > 0 log_fp = glob(join(self.test_out, 'log*.txt'))[0] self.assertTrue(getsize(log_fp) > 0) # parse the otu table otu_table = load_table(otu_table_fp) expected_sample_ids = [ 'f1', 'f2', 'f3', 'f4', 'p1', 'p2', 't1', 't2', 'not16S.1'] # sample IDs are as expected self.assertItemsEqual(otu_table.ids(), expected_sample_ids) # expected OTUs self.assertItemsEqual(otu_table.ids(axis='observation'), otu_map_otu_ids) # number of sequences in the full otu table equals the number of # input sequences number_seqs_in_otu_table = sum([v.sum() for v in otu_table.iter_data()]) self.assertEqual( number_seqs_in_otu_table, count_seqs(self.test_data['seqs'][0])[0])
def test_run_pick_de_novo_otus_parallel(self): """run_pick_de_novo_otus generates expected results in parallel """ self.params['assign_taxonomy'] = \ {'id_to_taxonomy_fp': self.test_data['refseqs_tax'][0], 'reference_seqs_fp': self.test_data['refseqs'][0]} self.params['align_seqs'] = \ {'template_fp': self.test_data['refseqs_aligned'][0]} self.params['filter_alignment'] = \ {'lane_mask_fp': self.test_data['refseqs_aligned_lanemask'][0]} actual_tree_fp, actual_otu_table_fp = run_pick_de_novo_otus( self.test_data['seqs'][0], self.test_out, call_commands_serially, self.params, self.qiime_config, parallel=True, status_update_callback=no_status_updates) input_file_basename = splitext(split(self.test_data['seqs'][0])[1])[0] otu_map_fp = join(self.test_out, 'uclust_picked_otus', '%s_otus.txt' % input_file_basename) alignment_fp = join(self.test_out, 'pynast_aligned_seqs', '%s_rep_set_aligned.fasta' % input_file_basename) failures_fp = join(self.test_out, 'pynast_aligned_seqs', '%s_rep_set_failures.fasta' % input_file_basename) taxonomy_assignments_fp = join(self.test_out, 'uclust_assigned_taxonomy', '%s_rep_set_tax_assignments.txt' % input_file_basename) otu_table_fp = join(self.test_out, 'otu_table.biom') tree_fp = join(self.test_out, 'rep_set.tre') self.assertEqual(actual_tree_fp, tree_fp) self.assertEqual(actual_otu_table_fp, otu_table_fp) # Number of OTUs falls within a range that was manually # confirmed otu_map_lines = list(open(otu_map_fp)) num_otus = len(otu_map_lines) otu_map_otu_ids = [o.split()[0] for o in otu_map_lines] self.assertEqual(num_otus, 14) # all otus get taxonomy assignments taxonomy_assignment_lines = list(open(taxonomy_assignments_fp)) self.assertEqual(len(taxonomy_assignment_lines), num_otus) # number of seqs which aligned + num of seqs which failed to # align sum to the number of OTUs self.assertEqual( count_seqs(alignment_fp)[0] + count_seqs(failures_fp)[0], num_otus) # number of tips in the tree equals the number of sequences that # aligned with open(tree_fp) as f: tree = TreeNode.from_newick(f) self.assertEqual(len(list(tree.tips())), count_seqs(alignment_fp)[0]) # parse the otu table otu_table = load_table(otu_table_fp) expected_sample_ids = [ 'f1', 'f2', 'f3', 'f4', 'p1', 'p2', 't1', 't2', 'not16S.1'] # sample IDs are as expected self.assertItemsEqual(otu_table.ids(), expected_sample_ids) # otu ids are as expected self.assertItemsEqual(otu_table.ids(axis='observation'), otu_map_otu_ids) # number of sequences in the full otu table equals the number of # input sequences number_seqs_in_otu_table = sum([v.sum() for v in otu_table.iter_data()]) self.assertEqual( number_seqs_in_otu_table, count_seqs(self.test_data['seqs'][0])[0]) # Check that the log file is created and has size > 0 log_fp = glob(join(self.test_out, 'log*.txt'))[0] self.assertTrue(getsize(log_fp) > 0)