#!/usr/bin/env python # ----------------------------------------------------------------------------- # Copyright (c) 2011-2017, The BIOM Format Development Team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file COPYING.txt, distributed with this software. # ----------------------------------------------------------------------------- import os from io import StringIO import json from unittest import TestCase, main from tempfile import NamedTemporaryFile import numpy as np import numpy.testing as npt from biom.parse import (generatedby, MetadataMap, parse_biom_table, parse_uc, load_table, save_table) from biom.table import Table from biom.util import __version__ from biom.tests.long_lines import (uc_empty, uc_invalid_id, uc_minimal, uc_lib_minimal, uc_seed_hits, uc_mixed_hits, uc_underscores_in_sample_id) import h5py __author__ = "Justin Kuczynski" __copyright__ = "Copyright 2011-2017, The BIOM Format Development Team" __credits__ = ["Justin Kuczynski", "Daniel McDonald", "Adam Robbins-Pianka", "Jose Antonio Navas Molina"] __license__ = "BSD" __url__ = "http://biom-format.org" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" class ParseTests(TestCase): """Tests of parse functions""" def setUp(self): """define some top-level data""" self.legacy_otu_table1 = legacy_otu_table1 self.otu_table1 = otu_table1 self.otu_table1_floats = otu_table1_floats self.files_to_remove = [] self.biom_minimal_sparse = biom_minimal_sparse self.classic_otu_table1_w_tax = classic_otu_table1_w_tax.split('\n') self.classic_otu_table1_no_tax = classic_otu_table1_no_tax.split('\n') self.classic_table_with_complex_metadata = \ classic_table_with_complex_metadata.split('\n') def test_from_tsv_bug_854(self): data = StringIO('#FeatureID\tSample1') exp = Table([], [], ['Sample1']) obs = Table.from_tsv(data, None, None, lambda x: x) self.assertEqual(obs, exp) def test_generatedby(self): """get a generatedby string""" exp = "BIOM-Format %s" % __version__ obs = generatedby() self.assertEqual(obs, exp) def test_metadata_map(self): """MetadataMap functions as expected This method is ported from QIIME (http://www.qiime.org). QIIME is a GPL project, but we obtained permission from the authors of this method to port it to the BIOM Format project (and keep it under BIOM's BSD license). """ s1 = ['#sample\ta\tb', '#comment line to skip', 'x \t y \t z ', ' ', '#more skip', 'i\tj\tk'] exp = ([['x', 'y', 'z'], ['i', 'j', 'k']], ['sample', 'a', 'b'], ['comment line to skip', 'more skip']) exp = {'x': {'a': 'y', 'b': 'z'}, 'i': {'a': 'j', 'b': 'k'}} obs = MetadataMap.from_file(s1) self.assertEqual(obs, exp) # check that we strip double quotes by default s2 = ['#sample\ta\tb', '#comment line to skip', '"x "\t" y "\t z ', ' ', '"#more skip"', 'i\t"j"\tk'] obs = MetadataMap.from_file(s2) self.assertEqual(obs, exp) def test_metadata_map_w_map_fs(self): """MetadataMap functions as expected w process_fns This method is ported from QIIME (http://www.qiime.org). QIIME is a GPL project, but we obtained permission from the authors of this method to port it to the BIOM Format project (and keep it under BIOM's BSD license). """ s1 = ['#sample\ta\tb', '#comment line to skip', 'x \t y \t z ', ' ', '#more skip', 'i\tj\tk'] exp = ([['x', 'y', 'z'], ['i', 'j', 'k']], ['sample', 'a', 'b'], ['comment line to skip', 'more skip']) exp = {'x': {'a': 'y', 'b': 'zzz'}, 'i': {'a': 'j', 'b': 'kkk'}} process_fns = {'b': lambda x: x * 3} obs = MetadataMap.from_file(s1, process_fns=process_fns) self.assertEqual(obs, exp) def test_metadata_map_w_header(self): """MetadataMap functions as expected w user-provided header This method is ported from QIIME (http://www.qiime.org). QIIME is a GPL project, but we obtained permission from the authors of this method to port it to the BIOM Format project (and keep it under BIOM's BSD license). """ # number of user-provided headers matches number of columns, and no # header line in file s1 = ['#comment line to skip', 'x \t y \t z ', ' ', '#more skip', 'i\tj\tk'] exp = ([['x', 'y', 'z'], ['i', 'j', 'k']], ['sample', 'a', 'b'], ['comment line to skip', 'more skip']) exp = {'x': {'a': 'y', 'b': 'z'}, 'i': {'a': 'j', 'b': 'k'}} header = ['sample', 'a', 'b'] obs = MetadataMap.from_file(s1, header=header) self.assertEqual(obs, exp) # number of user-provided headers is fewer than number of columns, and # no header line in file s1 = ['#comment line to skip', 'x \t y \t z ', ' ', '#more skip', 'i\tj\tk'] exp = ([['x', 'y', 'z'], ['i', 'j', 'k']], ['sample', 'a'], ['comment line to skip', 'more skip']) exp = {'x': {'a': 'y'}, 'i': {'a': 'j'}} header = ['sample', 'a'] obs = MetadataMap.from_file(s1, header=header) self.assertEqual(obs, exp) # number of user-provided headers is fewer than number of columns, and # header line in file (overridden by user-provided) s1 = ['#sample\ta\tb', '#comment line to skip', 'x \t y \t z ', ' ', '#more skip', 'i\tj\tk'] exp = ([['x', 'y', 'z'], ['i', 'j', 'k']], ['sample', 'a'], ['comment line to skip', 'more skip']) exp = {'x': {'a': 'y'}, 'i': {'a': 'j'}} header = ['sample', 'a'] obs = MetadataMap.from_file(s1, header=header) self.assertEqual(obs, exp) def test_parse_biom_json(self): """test the biom otu table parser""" # light test. this code is used thoroughly within the other # parse_biom_table methods tab1_fh = json.load(StringIO(self.biom_minimal_sparse)) tab = Table.from_json(tab1_fh) npt.assert_equal(tab.ids(), ('Sample1', 'Sample2', 'Sample3', 'Sample4', 'Sample5', 'Sample6')) npt.assert_equal(tab.ids(axis='observation'), ('GG_OTU_1', 'GG_OTU_2', 'GG_OTU_3', 'GG_OTU_4', 'GG_OTU_5')) self.assertEqual(tab.metadata(), None) self.assertEqual(tab.metadata(axis='observation'), None) tab = parse_biom_table(StringIO(self.biom_minimal_sparse)) npt.assert_equal(tab.ids(), ('Sample1', 'Sample2', 'Sample3', 'Sample4', 'Sample5', 'Sample6')) npt.assert_equal(tab.ids(axis='observation'), ('GG_OTU_1', 'GG_OTU_2', 'GG_OTU_3', 'GG_OTU_4', 'GG_OTU_5')) self.assertEqual(tab.metadata(), None) self.assertEqual(tab.metadata(axis='observation'), None) tablestring = '''{ "id":null, "format": "Biological Observation Matrix 0.9.1-dev", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "QIIME revision XYZ", "date": "2011-12-19T19:00:00", "rows":[ {"id":"GG_OTU_1", "metadata":null}, {"id":"GG_OTU_2", "metadata":null}, {"id":"GG_OTU_3", "metadata":null}, {"id":"GG_OTU_4", "metadata":null}, {"id":"GG_OTU_5", "metadata":null} ], "columns": [ {"id":"Sample1", "metadata":null}, {"id":"Sample2", "metadata":null}, {"id":"Sample3", "metadata":null}, {"id":"Sample4", "metadata":null}, {"id":"Sample5", "metadata":null}, {"id":"Sample6", "metadata":null} ], "matrix_type": "dense", "matrix_element_type": "int", "shape": [5,6], "data": [[0,0,1,0,0,0], [5,1,0,2,3,1], [0,0,1,4,2,0], [2,1,1,0,0,1], [0,1,1,0,0,0]] }''' tbs_fh = json.load(StringIO(tablestring)) tab1 = Table.from_json(tbs_fh) tab2 = parse_biom_table(tablestring) self.assertEqual(tab1, tab2) def test_parse_biom_table_subset(self): """test the biom table parser subsetting""" tab = parse_biom_table(StringIO(self.biom_minimal_sparse), ids=['Sample1', 'Sample3', 'Sample5', 'Sample6']) npt.assert_equal(tab.ids(), ('Sample1', 'Sample3', 'Sample5', 'Sample6')) npt.assert_equal(tab.ids(axis='observation'), ('GG_OTU_1', 'GG_OTU_2', 'GG_OTU_3', 'GG_OTU_4', 'GG_OTU_5')) self.assertEqual(tab.metadata(), None) self.assertEqual(tab.metadata(axis='observation'), None) tab = parse_biom_table(StringIO(self.biom_minimal_sparse), ids=['GG_OTU_2', 'GG_OTU_3', 'GG_OTU_5'], axis='observation') npt.assert_equal(tab.ids(), ('Sample1', 'Sample2', 'Sample3', 'Sample4', 'Sample5', 'Sample6',)) npt.assert_equal(tab.ids(axis='observation'), ('GG_OTU_2', 'GG_OTU_3', 'GG_OTU_5')) self.assertEqual(tab.metadata(), None) self.assertEqual(tab.metadata(axis='observation'), None) def test_parse_adjacency_weird_input(self): with self.assertRaisesRegex(ValueError, "Not sure"): Table.from_adjacency({'foo', 'bar'}) def test_parse_adjacency_bad_input(self): with self.assertRaisesRegex(ValueError, "Does not appear"): Table.from_adjacency(['a\tb\tc\n', 'd\te\tf\n']) with self.assertRaisesRegex(ValueError, "Does not appear"): Table.from_adjacency(['a\tb\n', 'd\te\n']) with self.assertRaises(AssertionError): Table.from_adjacency(['a\tb\t1\n', 'd\te\n']) def test_parse_adjacency_table_header(self): lines = ['#OTU ID\tSampleID\tvalue\n', 'O1\tS1\t10\n', 'O4\tS2\t1\n', 'O3\tS3\t2\n', 'O4\tS1\t5\n', 'O2\tS2\t3\n'] exp = Table(np.array([[10, 0, 0], [0, 3, 0], [0, 0, 2], [5, 1, 0]]), ['O1', 'O2', 'O3', 'O4'], ['S1', 'S2', 'S3']) obs = Table.from_adjacency(''.join(lines)) self.assertEqual(obs, exp) def test_parse_adjacency_table_no_header(self): lines = ['O1\tS1\t10\n', 'O4\tS2\t1\n', 'O3\tS3\t2\n', 'O4\tS1\t5\n', 'O2\tS2\t3\n'] exp = Table(np.array([[10, 0, 0], [0, 3, 0], [0, 0, 2], [5, 1, 0]]), ['O1', 'O2', 'O3', 'O4'], ['S1', 'S2', 'S3']) obs = Table.from_adjacency(''.join(lines)) self.assertEqual(obs, exp) def test_parse_biom_table_hdf5(self): """Make sure we can parse a HDF5 table through the same loader""" cwd = os.getcwd() if '/' in __file__[1:]: os.chdir(__file__.rsplit('/', 1)[0]) Table.from_hdf5(h5py.File('test_data/test.biom', 'r')) os.chdir(cwd) def test_save_table_filepath(self): t = Table(np.array([[0, 1, 2], [3, 4, 5]]), ['a', 'b'], ['c', 'd', 'e']) with NamedTemporaryFile() as tmpfile: save_table(t, tmpfile.name) obs = load_table(tmpfile.name) self.assertEqual(obs, t) def test_load_table_filepath(self): cwd = os.getcwd() if '/' in __file__[1:]: os.chdir(__file__.rsplit('/', 1)[0]) load_table('test_data/test.biom') os.chdir(cwd) def test_load_table_inmemory(self): cwd = os.getcwd() if '/' in __file__[1:]: os.chdir(__file__.rsplit('/', 1)[0]) load_table(h5py.File('test_data/test.biom', 'r')) os.chdir(cwd) def test_load_table_inmemory_json(self): cwd = os.getcwd() if '/' in __file__[1:]: os.chdir(__file__.rsplit('/', 1)[0]) load_table(open('test_data/test.json')) os.chdir(cwd) def test_load_table_inmemory_stringio(self): load_table(StringIO('\n'.join(self.classic_otu_table1_no_tax))) def test_parse_biom_table(self): """tests for parse_biom_table when we do not have h5py""" # This is a TSV as a list of lines t = parse_biom_table(self.classic_otu_table1_no_tax) # Test TSV as a list of lines t_tsv_str = t.to_tsv() t_tsv_lines = t_tsv_str.splitlines() t_tsv = parse_biom_table(t_tsv_lines) self.assertEqual(t, t_tsv) # Test TSV as a file-like object t_tsv_stringio = StringIO(t_tsv_str) t_tsv = parse_biom_table(t_tsv_stringio) self.assertEqual(t, t_tsv) # Test JSON as a list of lines t_json_str = t.to_json('asd') t_json_lines = t_json_str.splitlines() t_json = parse_biom_table(t_json_lines) self.assertEqual(t, t_json) # Test JSON as a file-like object t_json_str = t.to_json('asd') t_json_stringio = StringIO(t_json_str) t_json = parse_biom_table(t_json_stringio) self.assertEqual(t, t_json) def test_parse_biom_table_with_hdf5(self): """tests for parse_biom_table when we have h5py""" # We will round-trip the HDF5 file to several different formats, and # make sure we can recover the same table using parse_biom_table if '/' in __file__[1:]: os.chdir(__file__.rsplit('/', 1)[0]) t = parse_biom_table(h5py.File('test_data/test.biom', 'r')) # These things are not round-trippable using the general-purpose # parse_biom_table function t._sample_metadata = None t._observation_metadata = None t.type = None # Test TSV as a list of lines t_tsv_str = t.to_tsv() t_tsv_lines = t_tsv_str.splitlines() t_tsv = parse_biom_table(t_tsv_lines) self.assertEqual(t, t_tsv) # Test TSV as a file-like object t_tsv_stringio = StringIO(t_tsv_str) t_tsv = parse_biom_table(t_tsv_stringio) self.assertEqual(t, t_tsv) # Test JSON as a list of lines t_json_str = t.to_json('asd') t_json_lines = t_json_str.splitlines() t_json = parse_biom_table(t_json_lines) self.assertEqual(t, t_json) # Test JSON as a file-like object t_json_str = t.to_json('asd') t_json_stringio = StringIO(t_json_str) t_json = parse_biom_table(t_json_stringio) self.assertEqual(t, t_json) def test_empty_metadata_inconsistent_handling(self): oids = list('bacd') sids = list('YXZ') mat = np.array([[2, 1, 0], [0, 5, 0], [0, 3, 0], [1, 2, 0]]) A = Table(mat, oids, sids, observation_metadata=[{}, {}, {}, {}], sample_metadata=[{}, {}, {}]) B = Table(mat, oids, sids) self.assertEqual(A, B) legacy_otu_table1 = """# some comment goes here #OTU ID Fing Key NA Consensus Lineage 0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propioniba\ cterineae; Propionibacterium 1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; La\ ctobacillales; Lactobacillales; Streptococcaceae; Streptococcus 7 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniace\ ae; Corynebacteriaceae 3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; St\ aphylococcaceae 4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors """ otu_table1 = """# Some comment OTU ID Fing Key NA Consensus Lineage 0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propioniba\ cterineae; Propionibacterium # some other comment 1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; La\ ctobacillales; Lactobacillales; Streptococcaceae; Streptococcus 7 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniace\ ae; Corynebacteriaceae # comments # everywhere! 3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; St\ aphylococcaceae 4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors """ otu_table1_floats = """# Some comment OTU ID Fing Key NA Consensus Lineage 0 19111.0 44536.0 42.0 Bacteria; Actinobacteria; Actinobacteridae; Propio\ nibacterineae; Propionibacterium # some other comment 1 1216.0 3500.0 6.0 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; La\ ctobacillales; Lactobacillales; Streptococcaceae; Streptococcus 7 1803.0 1184.0 2.0 Bacteria; Actinobacteria; Actinobacteridae; Gordoniace\ ae; Corynebacteriaceae # comments # everywhere! 3 1722.1 4903.2 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; St\ aphylococcaceae 4 589.6 2074.4 34.5 Bacteria; Cyanobacteria; Chloroplasts; vectors """ classic_table_with_complex_metadata = """# some comment #OTU ID sample1 sample2 KEGG_Pathways K05842 1.0 3.5 rank1A; rank2A|rank1B; rank2B K05841 2.0 4.5 Environmental Information Processing; K00508 0.0 0.0 Metabolism; Lipid Metabolism; Linoleic acid metabolism K00500 0.5 0.5 Metabolism; Amino Acid Metabolism; Phenylalanine metabolism|Me\ tabolism; Amino Acid Metabolism; Phenylalanine, tyrosine and tryptophan biosyn\ thesis K00507 0.0 0.0 Metabolism; Lipid Metabolism; Biosynthesis of unsaturated fatt\ y acids|Organismal Systems; Endocrine System; PPAR signaling pathway """ biom_minimal_sparse = """ { "id":null, "format": "Biological Observation Matrix v0.9", "format_url": "http://some_website/QIIME_MGRAST_dataformat_v0.9.html", "type": "OTU table", "generated_by": "QIIME revision XYZ", "date": "2011-12-19T19:00:00", "rows":[ {"id":"GG_OTU_1", "metadata":null}, {"id":"GG_OTU_2", "metadata":null}, {"id":"GG_OTU_3", "metadata":null}, {"id":"GG_OTU_4", "metadata":null}, {"id":"GG_OTU_5", "metadata":null} ], "columns": [ {"id":"Sample1", "metadata":null}, {"id":"Sample2", "metadata":null}, {"id":"Sample3", "metadata":null}, {"id":"Sample4", "metadata":null}, {"id":"Sample5", "metadata":null}, {"id":"Sample6", "metadata":null} ], "matrix_type": "sparse", "matrix_element_type": "int", "shape": [5, 6], "data":[[0,2,1], [1,0,5], [1,1,1], [1,3,2], [1,4,3], [1,5,1], [2,2,1], [2,3,4], [2,4,2], [3,0,2], [3,1,1], [3,2,1], [3,5,1], [4,1,1], [4,2,1] ] } """ classic_otu_table1_w_tax = """#Full OTU Counts #OTU ID PC.354 PC.355 PC.356 PC.481 PC.593 PC.607 PC.634 PC.635 PC.636\ \tConsensus Lineage 0 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 1 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 2 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Porphyromonadaceae;Parabacteroides 3 2 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 4 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 5 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 6 0 0 0 0 0 0 0 1 0 Root;Bacteria;Actinobacteria;Actinobac\ teria 7 0 0 2 0 0 0 0 0 2 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 8 1 1 0 2 4 0 0 0 0 Root;Bacteria;Firmicutes;Bacilli;Lacto\ bacillales;Lactobacillaceae;Lactobacillus 9 0 0 2 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 10 0 1 0 0 0 0 0 0 0 Root;Bacteria 11 0 0 0 0 0 0 1 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 12 0 0 0 0 0 0 1 0 0 Root;Bacteria;Bacteroidetes 13 1 0 0 1 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 14 0 0 1 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 15 0 0 0 0 1 0 0 0 0 Root;Bacteria 16 1 0 2 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 17 0 0 0 1 0 0 4 10 37 Root;Bacteria;Bacteroidetes 18 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 19 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes 20 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 21 0 0 0 0 0 0 2 3 2 Root;Bacteria;Bacteroidetes 22 0 0 0 0 2 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 23 14 1 14 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Bacilli;Lacto\ bacillales;Lactobacillaceae;Lactobacillus 24 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 25 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 26 0 0 0 0 0 0 0 1 1 Root;Bacteria;Bacteroidetes 27 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes 28 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 29 6 0 4 0 2 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 30 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes 31 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 32 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 33 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 34 0 0 0 0 0 0 8 10 2 Root;Bacteria 35 1 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 36 1 0 1 0 0 0 0 1 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 37 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 38 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 39 0 0 0 0 0 0 0 1 0 Root;Bacteria;Bacteroidetes;Bacteroid\ etes;Bacteroidales;Rikenellaceae;Alistipes 40 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 41 0 0 1 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 42 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes 43 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 44 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 45 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Erysipelotric\ hi;Erysipelotrichales;Erysipelotrichaceae;Coprobacillus 46 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes 47 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 48 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 49 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 50 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 51 0 1 0 0 0 0 0 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 52 0 2 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 53 0 0 0 0 0 0 2 0 1 Root;Bacteria;Proteobacteria;Deltaprot\ eobacteria 54 0 0 0 0 0 0 5 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Porphyromonadaceae;Parabacteroides 55 0 0 0 0 0 0 1 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae;Alistipes 56 0 0 0 0 0 1 0 0 0 Root;Bacteria;Bacteroidetes 57 0 0 0 0 0 0 0 1 0 Root;Bacteria 58 1 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 59 0 0 0 0 0 0 0 0 1 Root;Bacteria;Deferribacteres;Deferrib\ acteres;Deferribacterales;Deferribacteraceae;Mucispirillum 60 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 61 0 0 1 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 62 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 63 1 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 64 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 65 0 0 0 6 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 66 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 67 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 68 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 69 0 0 1 0 0 0 0 0 0 Root;Bacteria 70 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 71 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 72 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 73 0 0 0 0 0 5 0 0 0 Root;Bacteria;Bacteroidetes 74 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 75 1 0 1 0 0 0 0 0 0 Root;Bacteria;Bacteroidetes 76 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 77 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 78 1 0 1 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 79 2 3 8 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 80 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Porphyromonadaceae;Parabacteroides 81 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 82 0 0 0 0 0 2 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 83 0 0 0 1 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 84 1 0 0 0 0 0 0 2 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae;Ruminococcus 85 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae;Alistipes 86 0 0 0 0 0 0 0 1 0 Root;Bacteria 87 0 0 1 0 0 2 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 88 0 0 0 0 0 0 0 1 0 Root;Bacteria 89 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 90 0 0 0 9 0 0 3 0 0 Root;Bacteria;Firmicutes;Erysipelotric\ hi;Erysipelotrichales;Erysipelotrichaceae;Turicibacter 91 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Butyrivibrio 92 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 93 0 0 0 0 0 0 2 1 0 Root;Bacteria;Bacteroidetes 94 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 95 0 0 0 2 0 0 0 0 0 Root;Bacteria;Bacteroidetes 96 0 0 0 1 0 1 0 1 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 97 0 0 0 0 0 1 0 0 0 Root;Bacteria 98 0 0 0 0 0 0 0 1 0 Root;Bacteria 99 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 100 0 0 0 1 0 0 0 0 0 Root;Bacteria 101 0 0 0 3 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 102 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 103 0 1 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 104 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 105 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 106 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 107 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 108 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Incertae Sedis XIII;Anaerovorax 109 0 0 0 1 0 0 1 5 2 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae;Alistipes 110 0 0 0 0 0 2 0 0 0 Root;Bacteria;Actinobacteria;Actinobac\ teria;Coriobacteridae;Coriobacteriales;Coriobacterineae;Coriobacteriaceae;Olse\ nella 111 0 0 0 0 0 0 1 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 112 0 0 0 0 0 0 1 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 113 0 0 0 0 0 1 0 0 0 Root;Bacteria 114 0 0 0 0 0 1 0 0 0 Root;Bacteria 115 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes 116 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 117 1 0 2 0 0 6 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 118 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 119 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 120 1 3 1 2 1 9 2 4 5 Root;Bacteria;Bacteroidetes 121 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 122 0 0 0 1 0 2 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 123 0 0 0 0 0 0 1 0 0 Root;Bacteria;Actinobacteria;Actinobac\ teria;Coriobacteridae;Coriobacteriales;Coriobacterineae;Coriobacteriaceae 124 0 0 0 0 0 0 1 0 0 Root;Bacteria;Actinobacteria;Actinobac\ teria;Coriobacteridae;Coriobacteriales;Coriobacterineae;Coriobacteriaceae 125 0 0 0 0 0 0 1 0 0 Root;Bacteria;Bacteroidetes 126 0 0 2 0 0 0 0 1 0 Root;Bacteria 127 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 128 0 0 0 0 0 0 1 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 129 0 0 0 1 0 0 0 0 0 Root;Bacteria 130 0 0 0 0 5 2 0 0 0 Root;Bacteria;Proteobacteria;Epsilonpr\ oteobacteria;Campylobacterales;Helicobacteraceae;Helicobacter 131 0 0 1 3 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 132 0 0 0 0 1 0 0 0 0 Root;Bacteria 133 0 0 1 0 0 0 0 0 0 Root;Bacteria 134 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 135 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 136 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 137 0 0 0 0 0 0 0 1 0 Root;Bacteria 138 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 139 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 140 0 0 0 0 0 0 1 3 0 Root;Bacteria 141 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 142 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 143 0 0 1 0 0 0 0 0 0 Root;Bacteria 144 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 145 0 0 2 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 146 1 0 0 0 2 0 2 0 3 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 147 0 1 0 1 1 0 0 0 3 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 148 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes 149 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 150 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 151 0 0 0 1 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 152 0 0 0 1 0 0 1 2 19 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 153 0 2 1 2 0 0 1 1 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 154 2 18 0 1 0 0 21 4 4 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 155 0 0 0 0 0 5 9 5 3 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae;Alistipes 156 0 0 1 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 157 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 158 1 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 159 0 0 0 0 0 0 0 1 1 Root;Bacteria;Bacteroidetes 160 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 161 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 162 0 0 0 0 0 3 5 2 6 Root;Bacteria;Deferribacteres;Deferrib\ acteres;Deferribacterales;Deferribacteraceae;Mucispirillum 163 0 0 0 0 0 0 0 0 1 Root;Bacteria 164 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 165 2 1 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 166 0 0 0 0 0 0 0 1 0 Root;Bacteria 167 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 168 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 169 0 2 0 7 0 0 0 2 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 170 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 171 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 172 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 173 0 0 0 0 0 1 0 0 0 Root;Bacteria 174 1 0 0 0 10 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Peptostreptococcaceae;Peptostreptococcaceae Incertae Sedis 175 0 0 0 0 1 0 0 0 0 Root;Bacteria;Bacteroidetes 176 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 177 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia 178 0 0 0 2 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 179 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 180 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 181 1 4 2 6 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 182 0 0 0 0 0 1 0 0 0 Root;Bacteria 183 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia 184 0 0 0 1 0 0 3 1 0 Root;Bacteria;Bacteroidetes 185 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 186 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 187 0 1 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 188 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 189 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 190 0 0 0 0 0 0 0 1 0 Root;Bacteria 191 2 1 10 2 24 0 0 1 1 Root;Bacteria 192 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Bacilli;Lacto\ bacillales;Streptococcaceae;Streptococcus 193 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Butyrivibrio 194 0 0 2 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae;Acetanaerobacterium 195 0 0 0 0 0 1 0 0 0 Root;Bacteria 196 0 0 0 0 0 1 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 197 0 1 0 0 0 0 0 0 0 Root;Bacteria 198 0 2 0 0 0 1 0 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales 199 0 0 0 0 0 1 1 0 0 Root;Bacteria 200 0 0 0 2 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 201 0 0 0 1 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 202 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 203 0 2 2 4 0 5 1 5 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae;Alistipes 204 1 4 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 205 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 206 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 207 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 208 0 2 0 2 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 209 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 210 0 0 0 0 0 0 0 0 1 Root;Bacteria 211 1 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 212 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 213 0 0 0 0 0 0 0 2 0 Root;Bacteria;Firmicutes 214 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 215 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 216 0 0 0 0 0 0 0 1 0 Root;Bacteria;Bacteroidetes 217 0 0 0 0 0 2 0 1 0 Root;Bacteria 218 0 0 0 0 9 1 0 0 0 Root;Bacteria;Bacteroidetes 219 0 0 0 0 1 0 0 0 0 Root;Bacteria 220 1 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 221 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes 222 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 223 0 0 0 0 0 0 0 2 2 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 224 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 225 0 2 1 0 0 0 0 0 0 Root;Bacteria;Bacteroidetes 226 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 227 0 1 2 0 9 1 1 1 3 Root;Bacteria;Bacteroidetes 228 16 0 0 0 12 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 229 0 0 0 0 0 1 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Incertae Sedis XIII 230 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 231 0 19 2 0 2 0 3 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 232 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 233 0 0 0 0 1 0 0 0 0 Root;Bacteria;Bacteroidetes 234 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Bacilli;Lacto\ bacillales;Lactobacillaceae;Lactobacillus 235 0 1 1 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 236 0 0 0 0 0 2 0 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales 237 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 238 0 0 0 0 0 0 0 1 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae;Alistipes 239 0 0 0 0 0 1 0 0 0 Root;Bacteria 240 0 0 0 0 0 1 0 0 0 Root;Bacteria 241 0 0 0 0 0 0 2 0 0 Root;Bacteria;TM7;TM7_genera_incertae_\ sedis 242 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 243 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 244 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes 245 0 0 0 1 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 246 0 0 0 0 0 0 0 1 0 Root;Bacteria 247 0 0 1 0 0 0 0 0 0 Root;Bacteria;Bacteroidetes 248 1 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Bacilli;Lacto\ bacillales;Lactobacillaceae;Lactobacillus 249 1 0 0 0 0 0 0 0 0 Root;Bacteria 250 1 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 251 0 0 0 1 4 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 252 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 253 0 0 0 0 2 0 0 5 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 254 11 13 6 13 2 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 255 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 256 0 0 0 0 0 0 1 0 0 Root;Bacteria 257 0 0 0 0 0 0 5 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae;Alistipes 258 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 259 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 260 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 261 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 262 0 1 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Bryantella 263 0 0 0 0 1 0 0 0 0 Root;Bacteria 264 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 265 0 0 0 0 0 2 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 266 0 0 0 2 0 0 0 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae;Alistipes 267 1 0 0 5 17 20 0 0 0 Root;Bacteria 268 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 269 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 270 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 271 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 272 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 273 0 0 0 0 0 0 1 0 0 Root;Bacteria 274 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 275 0 0 0 0 0 0 1 0 0 Root;Bacteria;Verrucomicrobia;Verrucom\ icrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia 276 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 277 1 0 0 0 0 0 0 0 0 Root;Bacteria 278 0 0 0 0 0 1 0 0 0 Root;Bacteria 279 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 280 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 281 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 282 0 0 0 0 0 0 2 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Porphyromonadaceae;Parabacteroides 283 0 0 0 0 0 0 2 1 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 284 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 285 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 286 0 2 3 1 4 0 5 0 4 Root;Bacteria;Bacteroidetes 287 0 0 0 0 0 0 1 1 1 Root;Bacteria;Bacteroidetes 288 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 289 0 0 0 0 3 0 0 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 290 0 0 0 0 0 0 0 0 2 Root;Bacteria;Firmicutes;Bacilli;Bacil\ lales;Staphylococcaceae;Staphylococcus 291 0 0 0 0 1 0 0 0 0 Root;Bacteria 292 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 293 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 294 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 295 29 1 10 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 296 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 297 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 298 0 0 0 0 0 0 1 0 0 Root;Bacteria;Actinobacteria;Actinobac\ teria 299 0 0 0 0 0 0 1 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 300 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia 301 0 0 0 0 0 0 2 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 302 0 0 0 0 0 1 0 0 0 Root;Bacteria 303 0 0 0 0 0 0 0 0 1 Root;Bacteria 304 0 0 0 0 0 0 0 1 0 Root;Bacteria;Bacteroidetes 305 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 306 0 0 0 0 0 0 0 0 1 Root;Bacteria 307 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 308 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae;Ruminococcaceae Incertae Sedis 309 0 0 0 1 0 0 0 0 0 Root;Bacteria;Actinobacteria;Actinobac\ teria;Coriobacteridae;Coriobacteriales;Coriobacterineae;Coriobacteriaceae;Deni\ trobacterium 310 0 0 1 0 0 0 0 0 0 Root;Bacteria 311 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 312 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 313 0 1 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Porphyromonadaceae;Parabacteroides 314 0 0 1 0 0 0 0 0 0 Root;Bacteria;Bacteroidetes 315 1 3 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 316 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 317 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 318 0 0 0 0 0 1 0 0 0 Root;Bacteria;Proteobacteria 319 0 2 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 320 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 321 0 0 0 0 0 0 0 0 1 Root;Bacteria 322 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 323 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 324 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 325 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 326 0 0 0 0 4 0 0 0 2 Root;Bacteria;Firmicutes;Erysipelotric\ hi;Erysipelotrichales;Erysipelotrichaceae;Erysipelotrichaceae Incertae Sedis 327 0 0 0 0 0 0 0 1 0 Root;Bacteria;Bacteroidetes 328 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 329 2 2 0 1 0 0 0 0 0 Root;Bacteria;Bacteroidetes 330 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes 331 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes 332 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 333 0 0 0 0 0 6 0 3 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 334 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 335 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 336 0 0 1 0 0 0 0 0 0 Root;Bacteria 337 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 338 0 0 0 0 0 0 0 1 0 Root;Bacteria 339 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 340 0 0 2 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 341 0 0 1 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 342 0 0 0 0 0 1 0 0 0 Root;Bacteria 343 0 0 0 0 0 0 0 0 1 Root;Bacteria;Actinobacteria;Actinobac\ teria;Coriobacteridae;Coriobacteriales;Coriobacterineae;Coriobacteriaceae 344 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 345 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 346 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 347 0 0 0 1 0 0 0 0 0 Root;Bacteria 348 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 349 0 0 0 0 0 0 1 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 350 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 351 0 0 0 0 2 2 1 4 1 Root;Bacteria;Bacteroidetes 352 3 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 353 0 4 4 0 1 2 0 2 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 354 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 355 0 0 0 0 0 0 0 1 0 Root;Bacteria 356 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 357 0 0 0 4 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 358 0 0 1 0 0 0 0 0 0 Root;Bacteria 359 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 360 0 0 1 0 0 0 0 1 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 361 2 0 2 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 362 1 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 363 0 0 0 0 0 1 0 1 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Rikenellaceae 364 1 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 365 0 0 0 0 0 2 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 366 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Roseburia 367 0 0 0 0 1 0 0 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 368 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 369 0 0 0 0 0 1 0 0 0 Root;Bacteria 370 2 1 0 5 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 371 1 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 372 0 1 0 0 0 0 0 0 0 Root;Bacteria 373 0 1 0 0 0 0 3 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Clostridiaceae;Clostridiaceae 1;Clostridium 374 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 375 0 0 0 0 0 0 4 0 0 Root;Bacteria;Firmicutes;Erysipelotric\ hi;Erysipelotrichales;Erysipelotrichaceae;Erysipelotrichaceae Incertae Sedis 376 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 377 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 378 0 0 0 0 0 0 0 0 1 Root;Bacteria;Bacteroidetes 379 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Ruminococcaceae 380 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Bacilli;Bacil\ lales;Staphylococcaceae;Staphylococcus 381 0 0 2 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 382 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 383 4 9 0 2 0 0 0 2 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 384 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 385 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Bacilli;Lacto\ bacillales;Carnobacteriaceae;Carnobacteriaceae 1 386 0 0 1 0 0 0 0 0 0 Root;Bacteria 387 0 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 388 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 389 0 1 0 0 0 0 0 0 0 Root;Bacteria 390 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 391 0 0 0 0 0 0 0 0 1 Root;Bacteria;Firmicutes 392 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 393 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 394 0 0 1 0 0 0 0 0 0 Root;Bacteria 395 1 1 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 396 2 0 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 397 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 398 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 399 0 0 0 0 0 0 13 0 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Bacteroidaceae;Bacteroides 400 0 0 0 0 0 0 1 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 401 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 402 0 1 0 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 403 0 0 0 0 0 0 0 1 0 Root;Bacteria;Bacteroidetes;Bacteroide\ tes;Bacteroidales;Prevotellaceae 404 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae;Lachnospiraceae Incertae Sedis 405 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 406 0 0 0 0 0 1 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 407 1 0 0 0 0 4 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 408 1 5 3 2 0 0 0 0 1 Root;Bacteria;Bacteroidetes 409 0 0 0 0 0 0 0 1 1 Root;Bacteria;Bacteroidetes 410 0 0 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 411 0 0 0 1 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 412 0 0 0 0 2 0 0 0 0 Root;Bacteria;Bacteroidetes 413 0 0 0 0 0 0 0 1 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales 414 1 0 1 0 0 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales;Lachnospiraceae 415 0 0 0 0 0 7 0 2 2 Root;Bacteria;Bacteroidetes 416 0 1 0 0 1 0 0 0 0 Root;Bacteria;Firmicutes;Clostridia;Cl\ ostridiales""" classic_otu_table1_no_tax = """#Full OTU Counts #OTU ID PC.354 PC.355 PC.356 PC.481 PC.593 PC.607 PC.634 PC.635 PC.636 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 2 0 0 0 0 0 0 0 0 1 3 2 1 0 0 0 0 0 0 0 4 1 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 1 6 0 0 0 0 0 0 0 1 0 7 0 0 2 0 0 0 0 0 2 8 1 1 0 2 4 0 0 0 0 9 0 0 2 0 0 0 0 0 0 10 0 1 0 0 0 0 0 0 0 11 0 0 0 0 0 0 1 0 0 12 0 0 0 0 0 0 1 0 0 13 1 0 0 1 0 1 0 0 0 14 0 0 1 1 0 0 0 0 0 15 0 0 0 0 1 0 0 0 0 16 1 0 2 0 0 0 0 0 0 17 0 0 0 1 0 0 4 10 37 18 0 1 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 1 20 0 0 0 0 1 0 0 0 0 21 0 0 0 0 0 0 2 3 2 22 0 0 0 0 2 0 1 0 0 23 14 1 14 1 0 0 0 0 0 24 1 0 0 0 0 0 0 0 0 25 0 0 0 1 0 0 0 0 0 26 0 0 0 0 0 0 0 1 1 27 0 0 0 0 0 0 0 0 1 28 0 1 0 0 0 0 0 0 0 29 6 0 4 0 2 0 0 0 0 30 0 0 0 0 0 1 0 0 0 31 1 0 0 0 0 0 0 0 0 32 0 0 0 0 1 0 0 0 0 33 0 0 0 1 0 0 0 0 0 34 0 0 0 0 0 0 8 10 2 35 1 0 1 0 0 0 0 0 0 36 1 0 1 0 0 0 0 1 1 37 0 0 0 0 0 1 0 0 0 38 0 0 1 0 0 0 0 0 0 39 0 0 0 0 0 0 0 1 0 40 0 0 1 0 0 0 0 0 0 41 0 0 1 0 0 0 0 1 0 42 0 0 0 0 0 1 0 0 0 43 0 0 0 0 0 1 0 0 0 44 0 0 1 0 0 0 0 0 0 45 1 0 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 0 1 47 0 0 0 1 0 0 0 0 0 48 0 0 0 0 1 0 0 0 0 49 0 0 0 1 0 0 0 0 0 50 0 1 0 0 0 0 0 0 0 51 0 1 0 0 0 0 0 0 0 52 0 2 0 0 0 0 0 0 0 53 0 0 0 0 0 0 2 0 1 54 0 0 0 0 0 0 5 0 0 55 0 0 0 0 0 0 1 0 0 56 0 0 0 0 0 1 0 0 0 57 0 0 0 0 0 0 0 1 0 58 1 0 1 0 0 0 0 0 0 59 0 0 0 0 0 0 0 0 1 60 0 0 0 0 0 0 0 1 0 61 0 0 1 0 0 0 0 1 0 62 0 0 1 0 0 0 0 0 0 63 1 0 1 0 0 0 0 0 0 64 0 0 0 0 0 0 0 0 1 65 0 0 0 6 0 0 0 1 0 66 0 0 1 0 0 0 0 0 0 67 0 0 1 0 0 0 0 0 0 68 1 0 0 0 0 0 0 0 0 69 0 0 1 0 0 0 0 0 0 70 0 0 0 0 0 1 0 0 0 71 0 0 1 0 0 0 0 0 0 72 0 0 0 0 0 1 0 0 0 73 0 0 0 0 0 5 0 0 0 74 0 0 0 1 0 0 0 0 0 75 1 0 1 0 0 0 0 0 0 76 0 0 0 1 0 0 0 0 0 77 0 0 0 1 0 0 0 0 0 78 1 0 1 1 0 0 0 0 0 79 2 3 8 0 1 0 0 0 0 80 0 0 0 0 0 0 0 0 1 81 1 0 0 0 0 0 0 0 0 82 0 0 0 0 0 2 0 0 0 83 0 0 0 1 0 0 0 1 0 84 1 0 0 0 0 0 0 2 0 85 0 0 0 0 0 0 0 0 1 86 0 0 0 0 0 0 0 1 0 87 0 0 1 0 0 2 0 1 0 88 0 0 0 0 0 0 0 1 0 89 0 0 1 0 0 0 0 0 0 90 0 0 0 9 0 0 3 0 0 91 0 0 0 1 0 0 0 0 0 92 0 0 0 0 0 0 1 0 0 93 0 0 0 0 0 0 2 1 0 94 0 0 0 0 0 0 0 1 0 95 0 0 0 2 0 0 0 0 0 96 0 0 0 1 0 1 0 1 1 97 0 0 0 0 0 1 0 0 0 98 0 0 0 0 0 0 0 1 0 99 0 0 0 1 0 0 0 0 0 100 0 0 0 1 0 0 0 0 0 101 0 0 0 3 0 0 0 0 0 102 0 1 0 0 0 0 0 0 0 103 0 1 0 0 0 0 1 0 0 104 0 0 0 0 0 1 0 0 0 105 0 1 0 0 0 0 0 0 0 106 0 0 0 0 0 1 0 0 0 107 0 0 0 0 0 1 0 0 0 108 0 0 0 0 0 0 1 0 0 109 0 0 0 1 0 0 1 5 2 110 0 0 0 0 0 2 0 0 0 111 0 0 0 0 0 0 1 0 0 112 0 0 0 0 0 0 1 0 0 113 0 0 0 0 0 1 0 0 0 114 0 0 0 0 0 1 0 0 0 115 0 0 0 0 0 1 0 0 0 116 0 1 0 0 0 0 0 0 0 117 1 0 2 0 0 6 0 0 0 118 0 0 0 1 0 0 0 0 0 119 0 0 0 0 0 0 0 1 0 120 1 3 1 2 1 9 2 4 5 121 0 0 0 0 0 0 0 1 0 122 0 0 0 1 0 2 0 0 0 123 0 0 0 0 0 0 1 0 0 124 0 0 0 0 0 0 1 0 0 125 0 0 0 0 0 0 1 0 0 126 0 0 2 0 0 0 0 1 0 127 0 0 0 0 0 1 0 0 0 128 0 0 0 0 0 0 1 0 0 129 0 0 0 1 0 0 0 0 0 130 0 0 0 0 5 2 0 0 0 131 0 0 1 3 0 0 0 0 0 132 0 0 0 0 1 0 0 0 0 133 0 0 1 0 0 0 0 0 0 134 0 0 0 0 0 0 0 0 1 135 0 0 1 0 0 0 0 0 0 136 1 0 0 0 0 0 0 0 0 137 0 0 0 0 0 0 0 1 0 138 0 0 1 0 0 0 0 0 0 139 1 0 0 0 0 0 0 0 0 140 0 0 0 0 0 0 1 3 0 141 0 0 0 0 1 0 0 0 0 142 0 0 0 0 1 0 0 0 0 143 0 0 1 0 0 0 0 0 0 144 0 0 0 0 0 1 0 0 0 145 0 0 2 0 0 0 0 0 0 146 1 0 0 0 2 0 2 0 3 147 0 1 0 1 1 0 0 0 3 148 0 0 0 0 0 1 0 0 0 149 0 0 0 0 0 0 0 1 0 150 0 0 0 0 1 0 0 0 0 151 0 0 0 1 0 0 0 1 0 152 0 0 0 1 0 0 1 2 19 153 0 2 1 2 0 0 1 1 1 154 2 18 0 1 0 0 21 4 4 155 0 0 0 0 0 5 9 5 3 156 0 0 1 0 0 0 0 1 0 157 0 0 1 0 0 0 0 0 0 158 1 0 1 0 0 0 0 0 0 159 0 0 0 0 0 0 0 1 1 160 0 0 0 0 0 0 1 0 0 161 0 0 1 0 0 0 0 0 0 162 0 0 0 0 0 3 5 2 6 163 0 0 0 0 0 0 0 0 1 164 0 0 0 0 0 1 0 0 0 165 2 1 1 0 0 0 0 0 0 166 0 0 0 0 0 0 0 1 0 167 1 0 0 0 0 0 0 0 0 168 0 0 0 1 0 0 0 0 0 169 0 2 0 7 0 0 0 2 0 170 0 0 0 1 0 0 0 0 0 171 0 0 0 1 0 0 0 0 0 172 1 0 0 0 0 0 0 0 0 173 0 0 0 0 0 1 0 0 0 174 1 0 0 0 10 0 0 0 0 175 0 0 0 0 1 0 0 0 0 176 0 0 0 0 0 1 0 0 0 177 0 0 0 1 0 0 0 0 0 178 0 0 0 2 0 0 0 0 0 179 0 0 0 1 0 0 0 0 0 180 0 0 0 0 1 0 0 0 0 181 1 4 2 6 0 0 0 0 0 182 0 0 0 0 0 1 0 0 0 183 0 0 0 0 0 0 1 0 0 184 0 0 0 1 0 0 3 1 0 185 0 0 0 0 0 0 0 0 1 186 0 0 1 0 0 0 0 0 0 187 0 1 0 0 0 0 0 0 1 188 0 0 0 0 0 0 0 1 0 189 0 0 0 1 0 0 0 0 0 190 0 0 0 0 0 0 0 1 0 191 2 1 10 2 24 0 0 1 1 192 0 0 0 0 0 1 0 0 0 193 0 0 0 0 0 1 0 0 0 194 0 0 2 0 0 0 0 0 0 195 0 0 0 0 0 1 0 0 0 196 0 0 0 0 0 1 0 1 0 197 0 1 0 0 0 0 0 0 0 198 0 2 0 0 0 1 0 0 0 199 0 0 0 0 0 1 1 0 0 200 0 0 0 2 0 0 0 0 0 201 0 0 0 1 0 1 0 0 0 202 0 0 0 0 0 0 1 0 0 203 0 2 2 4 0 5 1 5 0 204 1 4 0 1 0 0 0 0 0 205 0 0 0 0 0 0 0 1 0 206 0 1 0 0 0 0 0 0 0 207 0 0 0 0 0 0 0 1 0 208 0 2 0 2 0 0 0 1 0 209 0 0 1 0 0 0 0 0 0 210 0 0 0 0 0 0 0 0 1 211 1 0 0 1 0 0 0 0 0 212 0 0 0 0 0 0 0 0 1 213 0 0 0 0 0 0 0 2 0 214 0 0 0 0 0 0 0 1 0 215 0 0 0 0 0 0 0 1 0 216 0 0 0 0 0 0 0 1 0 217 0 0 0 0 0 2 0 1 0 218 0 0 0 0 9 1 0 0 0 219 0 0 0 0 1 0 0 0 0 220 1 0 0 0 1 0 0 0 0 221 0 0 0 0 0 0 0 1 0 222 0 1 0 0 0 0 0 0 0 223 0 0 0 0 0 0 0 2 2 224 0 0 0 1 0 0 0 0 0 225 0 2 1 0 0 0 0 0 0 226 0 0 0 0 0 1 0 0 0 227 0 1 2 0 9 1 1 1 3 228 16 0 0 0 12 0 0 0 0 229 0 0 0 0 0 1 1 0 0 230 0 0 0 1 0 0 0 0 0 231 0 19 2 0 2 0 3 0 0 232 0 0 0 0 0 0 1 0 0 233 0 0 0 0 1 0 0 0 0 234 0 0 0 0 1 0 0 0 0 235 0 1 1 0 1 0 0 0 0 236 0 0 0 0 0 2 0 0 0 237 0 0 0 0 1 0 0 0 0 238 0 0 0 0 0 0 0 1 0 239 0 0 0 0 0 1 0 0 0 240 0 0 0 0 0 1 0 0 0 241 0 0 0 0 0 0 2 0 0 242 0 0 0 0 0 0 1 0 0 243 0 0 0 0 0 0 1 0 0 244 0 0 0 0 0 0 0 0 1 245 0 0 0 1 0 0 0 1 0 246 0 0 0 0 0 0 0 1 0 247 0 0 1 0 0 0 0 0 0 248 1 0 0 1 0 0 0 0 0 249 1 0 0 0 0 0 0 0 0 250 1 0 0 0 0 0 0 1 0 251 0 0 0 1 4 0 0 0 0 252 0 0 0 1 0 0 0 0 0 253 0 0 0 0 2 0 0 5 0 254 11 13 6 13 2 0 0 0 0 255 0 0 0 0 0 1 0 0 0 256 0 0 0 0 0 0 1 0 0 257 0 0 0 0 0 0 5 0 0 258 0 0 1 0 0 0 0 0 0 259 0 0 0 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1 0 0 0 0 0 0 0 0 351 0 0 0 0 2 2 1 4 1 352 3 0 0 0 0 0 0 0 0 353 0 4 4 0 1 2 0 2 1 354 0 0 0 0 0 1 0 0 0 355 0 0 0 0 0 0 0 1 0 356 0 0 0 0 0 1 0 0 0 357 0 0 0 4 0 0 0 0 0 358 0 0 1 0 0 0 0 0 0 359 0 0 1 0 0 0 0 0 0 360 0 0 1 0 0 0 0 1 1 361 2 0 2 1 0 0 0 0 0 362 1 0 0 1 0 0 0 0 0 363 0 0 0 0 0 1 0 1 0 364 1 0 0 0 0 0 0 0 0 365 0 0 0 0 0 2 0 0 0 366 0 0 0 1 0 0 0 0 0 367 0 0 0 0 1 0 0 0 0 368 0 0 0 0 0 1 0 0 0 369 0 0 0 0 0 1 0 0 0 370 2 1 0 5 0 1 0 0 0 371 1 1 0 0 0 0 0 0 0 372 0 1 0 0 0 0 0 0 0 373 0 1 0 0 0 0 3 0 0 374 0 0 0 0 0 0 1 0 0 375 0 0 0 0 0 0 4 0 0 376 0 0 0 0 0 0 0 0 1 377 0 0 0 0 0 0 0 1 0 378 0 0 0 0 0 0 0 0 1 379 0 0 0 0 0 1 0 0 0 380 0 0 0 0 0 0 0 0 1 381 0 0 2 0 0 0 0 0 0 382 0 0 0 0 0 0 0 1 0 383 4 9 0 2 0 0 0 2 0 384 0 0 1 0 0 0 0 0 0 385 0 0 0 0 0 0 0 0 1 386 0 0 1 0 0 0 0 0 0 387 0 0 1 0 0 0 0 0 0 388 0 0 0 1 0 0 0 0 0 389 0 1 0 0 0 0 0 0 0 390 0 0 0 0 0 0 0 0 1 391 0 0 0 0 0 0 0 0 1 392 0 1 0 0 0 0 0 0 0 393 0 0 0 0 0 1 0 0 0 394 0 0 1 0 0 0 0 0 0 395 1 1 1 0 0 0 0 0 0 396 2 0 0 0 0 0 0 0 0 397 0 0 0 0 0 0 0 1 0 398 0 0 0 0 0 0 0 1 0 399 0 0 0 0 0 0 13 0 0 400 0 0 0 0 0 0 1 0 0 401 0 1 0 0 0 0 0 0 0 402 0 1 0 0 0 0 0 0 0 403 0 0 0 0 0 0 0 1 0 404 0 0 0 0 0 0 0 1 0 405 0 0 0 0 0 0 0 1 0 406 0 0 0 0 0 1 0 0 0 407 1 0 0 0 0 4 0 0 0 408 1 5 3 2 0 0 0 0 1 409 0 0 0 0 0 0 0 1 1 410 0 0 0 0 1 0 0 0 0 411 0 0 0 1 0 0 0 0 0 412 0 0 0 0 2 0 0 0 0 413 0 0 0 0 0 0 0 1 0 414 1 0 1 0 0 0 0 0 0 415 0 0 0 0 0 7 0 2 2 416 0 1 0 0 1 0 0 0 0""" class ParseUcTests(TestCase): def test_empty(self): """ empty uc file returns empty Table """ actual = parse_uc(uc_empty.split('\n')) expected = Table(np.array([[]]), observation_ids=[], sample_ids=[]) self.assertEqual(actual, expected) def test_minimal(self): """ single new seed observed """ actual = parse_uc(uc_minimal.split('\n')) expected = Table(np.array([[1.0]]), observation_ids=['f2_1539'], sample_ids=['f2']) self.assertEqual(actual, expected) def test_lib_minimal(self): """ single library seed observed """ actual = parse_uc(uc_lib_minimal.split('\n')) expected = Table(np.array([[1.0]]), observation_ids=['295053'], sample_ids=['f2']) self.assertEqual(actual, expected) def test_invalid(self): """ invalid query sequence identifier detected """ self.assertRaises(ValueError, parse_uc, uc_invalid_id.split('\n')) def test_seed_hits(self): """ multiple new seeds observed """ actual = parse_uc(uc_seed_hits.split('\n')) expected = Table(np.array([[2.0, 1.0], [0.0, 1.0]]), observation_ids=['f2_1539', 'f3_44'], sample_ids=['f2', 'f3']) self.assertEqual(actual, expected) def test_mixed_hits(self): """ new and library seeds observed """ actual = parse_uc(uc_mixed_hits.split('\n')) expected = Table(np.array([[2.0, 1.0], [0.0, 1.0], [1.0, 0.0]]), observation_ids=['f2_1539', 'f3_44', '295053'], sample_ids=['f2', 'f3']) self.assertEqual(actual, expected) def test_underscores_in_sample_id(self): """ sample id with underscores is correctly processed """ actual = parse_uc(uc_underscores_in_sample_id.split('\n')) expected = Table(np.array([[2.0, 1.0], [0.0, 1.0], [1.0, 0.0]]), observation_ids=['_f_2__1539', 'f_3_44', '295053'], sample_ids=['_f_2_', 'f_3']) self.assertEqual(actual, expected) if __name__ == '__main__': main()