test_parse.py

#!/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

from biom.parse import generatedby, MetadataMap, parse_biom_table, parse_uc
from biom.table import Table
from biom.util import HAVE_H5PY, __version__
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_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 = u'''{
            "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)

    @npt.dec.skipif(HAVE_H5PY is False, msg='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)

    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)

    @npt.dec.skipif(HAVE_H5PY is False, msg='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
        cwd = os.getcwd()
        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)


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 = u"""
    {
        "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	0	0	0	0	1	0
260	0	0	0	0	0	0	0	1	0
261	0	0	0	0	0	0	0	1	0
262	0	1	0	0	0	0	0	0	1
263	0	0	0	0	1	0	0	0	0
264	0	0	0	0	0	1	0	0	0
265	0	0	0	0	0	2	0	0	0
266	0	0	0	2	0	0	0	0	0
267	1	0	0	5	17	20	0	0	0
268	0	0	0	0	0	0	1	0	0
269	0	0	0	1	0	0	0	0	0
270	0	0	1	0	0	0	0	0	0
271	0	0	0	0	0	0	0	0	1
272	0	0	0	1	0	0	0	0	0
273	0	0	0	0	0	0	1	0	0
274	0	0	0	0	0	0	1	0	0
275	0	0	0	0	0	0	1	0	0
276	0	0	0	0	0	0	0	1	0
277	1	0	0	0	0	0	0	0	0
278	0	0	0	0	0	1	0	0	0
279	0	0	0	0	0	1	0	0	0
280	0	1	0	0	0	0	0	0	0
281	1	0	0	0	0	0	0	0	0
282	0	0	0	0	0	0	2	0	0
283	0	0	0	0	0	0	2	1	0
284	0	0	0	1	0	0	0	0	0
285	0	0	0	0	0	0	1	0	0
286	0	2	3	1	4	0	5	0	4
287	0	0	0	0	0	0	1	1	1
288	0	0	0	0	0	1	0	0	0
289	0	0	0	0	3	0	0	0	0
290	0	0	0	0	0	0	0	0	2
291	0	0	0	0	1	0	0	0	0
292	0	0	0	0	1	0	0	0	0
293	0	0	0	0	0	1	0	0	0
294	0	1	0	0	0	0	0	0	0
295	29	1	10	0	0	0	0	0	0
296	0	0	0	0	1	0	0	0	0
297	0	0	0	1	0	0	0	0	0
298	0	0	0	0	0	0	1	0	0
299	0	0	0	0	0	0	1	0	1
300	0	0	0	0	0	1	0	0	0
301	0	0	0	0	0	0	2	0	0
302	0	0	0	0	0	1	0	0	0
303	0	0	0	0	0	0	0	0	1
304	0	0	0	0	0	0	0	1	0
305	1	0	0	0	0	0	0	0	0
306	0	0	0	0	0	0	0	0	1
307	0	0	1	0	0	0	0	0	0
308	0	1	0	0	0	0	0	0	0
309	0	0	0	1	0	0	0	0	0
310	0	0	1	0	0	0	0	0	0
311	0	0	0	0	0	1	0	0	0
312	0	0	1	0	0	0	0	0	0
313	0	1	0	0	0	0	0	0	1
314	0	0	1	0	0	0	0	0	0
315	1	3	1	0	0	0	0	0	0
316	0	1	0	0	0	0	0	0	0
317	0	0	0	0	0	0	1	0	0
318	0	0	0	0	0	1	0	0	0
319	0	2	1	0	0	0	0	0	0
320	0	0	0	1	0	0	0	0	0
321	0	0	0	0	0	0	0	0	1
322	0	0	0	1	0	0	0	0	0
323	0	0	1	0	0	0	0	0	0
324	0	0	1	0	0	0	0	0	0
325	0	1	0	0	0	0	0	0	0
326	0	0	0	0	4	0	0	0	2
327	0	0	0	0	0	0	0	1	0
328	0	0	0	1	0	0	0	0	0
329	2	2	0	1	0	0	0	0	0
330	0	0	1	0	0	0	0	0	0
331	0	0	0	0	1	0	0	0	0
332	0	1	0	0	0	0	0	0	0
333	0	0	0	0	0	6	0	3	0
334	1	0	0	0	0	0	0	0	0
335	0	0	0	0	0	0	0	1	0
336	0	0	1	0	0	0	0	0	0
337	0	0	0	1	0	0	0	0	0
338	0	0	0	0	0	0	0	1	0
339	0	0	1	0	0	0	0	0	0
340	0	0	2	0	0	0	0	0	0
341	0	0	1	0	0	0	0	1	0
342	0	0	0	0	0	1	0	0	0
343	0	0	0	0	0	0	0	0	1
344	0	0	1	0	0	0	0	0	0
345	1	0	0	0	0	0	0	0	0
346	0	1	0	0	0	0	0	0	0
347	0	0	0	1	0	0	0	0	0
348	0	0	0	1	0	0	0	0	0
349	0	0	0	0	0	0	1	0	1
350	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)


# no hits or library seeds
uc_empty = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
"""

# label not in qiime post-split-libraries format
uc_invalid_id = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S	0	133	*	*	*	*	*	1539	*
"""

# contains single new (de novo) seed hit
uc_minimal = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S	0	133	*	*	*	*	*	f2_1539	*
"""

# contains single library (reference) seed hit
uc_lib_minimal = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
L	3	1389	*	*	*	*	*	295053	*
H	3	133	100.0	+	0	0	519I133M737I	f2_1539	295053
"""

# contains new seed (de novo) hits only
uc_seed_hits = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S	0	133	*	*	*	*	*	f2_1539	*
H	0	141	100.0	+	0	0	133M8D	f3_42	f2_1539
H	0	141	100.0	+	0	0	133M8D	f2_43	f2_1539
S	0	133	*	*	*	*	*	f3_44	*
"""

# contains library (reference) and new seed (de novo) hits
uc_mixed_hits = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S	0	133	*	*	*	*	*	f2_1539	*
H	0	141	100.0	+	0	0	133M8D	f3_42	f2_1539
H	0	141	100.0	+	0	0	133M8D	f2_43	f2_1539
S	0	133	*	*	*	*	*	f3_44	*
L	3	1389	*	*	*	*	*	295053	*
H	3	133	100.0	+	0	0	519I133M737I	f2_1539	295053
"""

if __name__ == '__main__':
    main()