#!/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 import numpy as np import numpy.testing as npt import pytest from biom.parse import (generatedby, MetadataMap, parse_biom_table, parse_uc, load_table) from biom.table import Table from biom.util import HAVE_H5PY, __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) if HAVE_H5PY: 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) @pytest.mark.skipif(HAVE_H5PY is False, reason='H5PY is not installed') 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')) os.chdir(cwd) @pytest.mark.skipif(HAVE_H5PY is False, reason='H5PY is not installed') 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) @pytest.mark.skipif(HAVE_H5PY is False, reason='H5PY is not installed') 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')) 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) @pytest.mark.skipif(HAVE_H5PY is False, reason='H5PY is not installed') 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')) # 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()