[FEATURE] Closes #1; table import

motu-tool · Nov 14, 2022 · 3ee25d0 · 3ee25d0
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,50 @@
+name: ci
+
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - name: checkout source
+      uses: actions/checkout@v2
+
+    - name: set up python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: install dependencies
+      run: python -m pip install --upgrade pip
+
+    - name: lint
+      run: |
+        pip install -q https://github.com/qiime2/q2lint/archive/master.zip
+        q2lint
+        pip install -q flake8
+        flake8
+  build-and-test:
+    needs: lint
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+    - name: checkout source
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: set up git repo for versioneer
+      run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+
+    - uses: qiime2/action-library-packaging@alpha1
+      with:
+        package-name: q2-motus
+        build-target: dev
+        additional-tests: py.test --pyargs q2_motus
+        library-token: ${{ secrets.LIBRARY_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -128,4 +128,5 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-q2_motus/tests/data/dev.ipynb
+q2_motus/tests/data/dev.ipynb
+dev.ipynb
diff --git a/Makefile b/Makefile
@@ -14,8 +14,9 @@ test-cov: all
 	py.test --cov=q2_motus
 
 install:
-	which motus  || pip install motu-profiler
-	which bwa || git clone https://github.com/lh3/bwa.git || cd bwa || make || cd .. || rm -rf bwa
+	if ! which motus > /dev/null; then pip install motu-profiler; fi
+	if ! which bwa > /dev/null; then git clone https://github.com/lh3/bwa.git && cd bwa && make && ln -s $(PWD)/bwa/bwa $(CONDA_PREFIX)/bin; fi
+
 	motus downloadDB
 	$(PYTHON) setup.py install
 

diff --git a/README.md b/README.md
@@ -43,6 +43,12 @@ qiime motus profile \
     --p-jobs 2
 ```
 
+## Optionaly, you can import precomputed, merged mOTU profiles
+**Attention**: precomupted mOTU table should be generated from full taxonomy `-q` flag and counts `-c` flag profiles. 
+
+``` 
+qiime motus import_table \
+
 ## Output 
 1. `table` - `FeatureTable[Frequency]` - A table of the counts of gene markers in samples.
 2. `taxonomy` - `FeatureData[Taxonomy]` -  A full taxonomy for each of the gene marker.

diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
@@ -0,0 +1,41 @@
+
+{% set data = load_setup_py_data() %}
+{% set version = data.get('version') or 'placehold' %}
+
+package:
+  name: q2-motus
+  version: {{ version }}
+
+source:
+  path: ../..
+
+build:
+  script: make install
+
+requirements:
+  host:
+    - python {{ python }}
+    - setuptools
+
+  run:
+    - python {{ python }}
+    - pandas {{ pandas }}
+    - qiime2 {{ qiime2_epoch }}.*
+    - q2-types {{ qiime2_epoch }}.*
+    - bwa
+
+test:
+  requires:
+    - qiime2 >={{ qiime2 }}
+    - q2-types >={{ q2_types }}
+    - pytest
+    - bwa
+
+  imports:
+    - q2_motus
+    - qiime2.plugins.motus
+
+about:
+  home: https://github.com/motu-tool/q2-mOTUs
+  license: BSD-3-Clause
+  license_family: BSD
diff --git a/q2_motus/__init__.py b/q2_motus/__init__.py
@@ -1,7 +1,13 @@
-from ._taxonomy import profile
+from ._taxonomy import profile, import_table
 from ._version import get_versions
 
 __version__ = get_versions()['version']
 del get_versions
 
-__all__ = ['profile']
+__all__ = ['profile', 'import_table']
+
+from .plugin_setup import (
+    MotusMergedAbundanceTable,
+    MotusMergedAbundanceFormat, 
+    MotusMergedAbundanceDirectoryFormat
+    )
diff --git a/q2_motus/_format.py b/q2_motus/_format.py
@@ -0,0 +1,47 @@
+from qiime2.plugin import model, ValidationError, TextFileFormat
+
+
+class MotusMergedAbundanceFormat(TextFileFormat):
+    def _equal_number_of_columns(self, n_lines):
+        call_params = {}
+        with self.open() as fh:
+            header_line = fh.readline()
+            param_line = header_line.split("#")[-1]
+            name, info = param_line.split()[0], param_line
+            call_params[name] = info
+            while header_line.startswith('# '):
+                header_line = fh.readline()
+                param_line = header_line.split("#")[-1]
+                name, info = param_line.split()[0], param_line
+                call_params[name] = info
+            if not "merge" in call_params["call:"]:
+                raise ValidationError("This is not a merged abundance file. Please, merge abundance files first.")
+            n_header_fields = len(header_line.split('\t'))
+            if n_header_fields < 3:
+                raise ValidationError(
+                    'No sample columns appear to be present.')
+            for idx, line in enumerate(fh, 2):
+                if n_lines is not None and idx > n_lines + 1:
+                    break
+                fields = line.strip().split('\t')
+                n_fields = len(fields)
+                if n_fields != n_header_fields:
+                    raise ValidationError(
+                        f'Number of columns on line {line} is inconsistent with '
+                        'the header line.')
+                for value in fields[2:]:
+                    try:
+                        value = int(value)
+                    except ValueError:
+                        raise ValidationError(
+                            f'Values in table must be int-able. Found: {value}'
+                        )
+
+    def _validate_(self, level):
+        level_to_n_lines = {'min': 5, 'max': None}
+        self._equal_number_of_columns(level_to_n_lines[level])
+
+MotusMergedAbundanceDirectoryFormat = model.SingleFileDirectoryFormat(
+    'MotusMergedAbundanceDirectoryFormat', 'table.tsv',
+    MotusMergedAbundanceFormat)
+
diff --git a/q2_motus/_taxonomy.py b/q2_motus/_taxonomy.py
@@ -88,12 +88,14 @@ def profile_sample(
 
     return cmd
 
-
-def load_table_extract_tax(tab_fp: str, ncbi: bool = False) -> Tuple[pd.DataFrame, pd.DataFrame]:
-    '''Converts merged mOTU table to feature table and taxonomy'''
+def load_motus_table(tab_fp: str) -> pd.DataFrame:
     df = pd.read_csv(tab_fp, sep='\t', index_col=0, skiprows=2)
+    return df 
+
+
+def extract_table_tax(df: pd.DataFrame, ncbi: bool = False) -> Tuple[pd.DataFrame, pd.DataFrame]:
     df = df.replace({0 : np.nan})
-    df.index = df.index.rename("Feature ID")
+    df.index.name = "Feature ID"
     if ncbi:
         df = df.rename(columns={"NCBI_tax_id" : "Taxon"})
     else:
@@ -159,5 +161,13 @@ def profile(
         _run_command(cmd)
 
         # output merged profiles as feature table
-        tab, tax = load_table_extract_tax(taxatable, ncbi_taxonomy)
-        return tab, tax
+        tab, tax = extract_table_tax(load_motus_table(taxatable), ncbi_taxonomy)
+        return tab, tax
+
+
+def import_table(
+    motus_table: pd.DataFrame, 
+    ncbi_taxonomy: bool = False) -> (pd.DataFrame, pd.DataFrame):
+
+    tab, tax = extract_table_tax(motus_table, ncbi=ncbi_taxonomy)
+    return tab, tax
diff --git a/q2_motus/plugin_setup.py b/q2_motus/plugin_setup.py
@@ -1,12 +1,15 @@
-import q2_motus
-
-from qiime2.plugin import (Int, Range, Str, Bool, Choices, Plugin, Citations) 
-
-from q2_motus._taxonomy import profile
-from q2_types.sample_data import SampleData
+import pandas as pd 
 from q2_types.feature_data import FeatureData, Taxonomy
-from q2_types.per_sample_sequences import SequencesWithQuality, PairedEndSequencesWithQuality
 from q2_types.feature_table import FeatureTable, Frequency
+from q2_types.per_sample_sequences import (PairedEndSequencesWithQuality,
+                                           SequencesWithQuality)
+from q2_types.sample_data import SampleData
+from qiime2.plugin import (Bool, Choices, Citations, Int, Plugin, Range,
+                           SemanticType, Str)
+
+import q2_motus
+from q2_motus._taxonomy import import_table, profile
+from q2_motus._format import MotusMergedAbundanceFormat, MotusMergedAbundanceDirectoryFormat
 
 citations = Citations.load('citations.bib', package='q2_motus')
 
@@ -22,6 +25,24 @@
 )
 
 
+MotusMergedAbundanceTable = SemanticType('MotusMergedAbundanceTable')
+plugin.register_semantic_types(MotusMergedAbundanceTable)
+
+plugin.register_formats(MotusMergedAbundanceFormat,
+                        MotusMergedAbundanceDirectoryFormat)
+plugin.register_semantic_type_to_format(MotusMergedAbundanceTable, 
+                                        MotusMergedAbundanceDirectoryFormat)
+
+def _motus_to_df(path):
+    result = pd.read_csv(str(path), sep='\t', header=0, index_col=0, skiprows=2)
+    result.index.name = 'FeatureID'
+    return result
+
+@plugin.register_transformer
+def _1(data: MotusMergedAbundanceFormat) -> pd.DataFrame:
+    return _motus_to_df(data)
+
+
 plugin.methods.register_function(
     function=profile,
     inputs={"samples": SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]},
@@ -36,10 +57,10 @@
                 "reference_genomes": Bool,
                 "ncbi_taxonomy": Bool,
                 "jobs": Int % Range(1, None)},
-    name="mOTU paired end profiler",
-    description="Executes a taxonomical classification of paired-end sample.",
+    name="mOTU profiler",
+    description="Executes a taxonomical classification of a sample.",
     citations=[citations["Milanese2019-gw"]],
-    input_descriptions={"samples": "The paired-end samples to be classified."},
+    input_descriptions={"samples": "Samples for profiling."},
     parameter_descriptions={"threads": "The number of threads to use. We suggest using 4-8 threads.",
                             "min_alen": "Minimum alignment length.",
                             "marker_gene_cutoff": "Minimum number of marker genes to be considered a species." 
@@ -53,4 +74,23 @@
                             "jobs": "The number of jobs to use for the computation. Each job uses n threads from the threads parameter."},
     output_descriptions={"table": "The feature table with counts of marker genes in samples.",
                          "taxonomy": "The taxonomy."}
-)
+)
+
+
+plugin.methods.register_function(
+    function=import_table,
+    inputs={"motus_table": MotusMergedAbundanceTable},
+    outputs=[
+        ("table", FeatureTable[Frequency]), 
+        ("taxonomy", FeatureData[Taxonomy])
+        ],
+    parameters={"ncbi_taxonomy": Bool},
+    name="mOTU table importer",
+    description="Imports precomputed mOTU table to QIIME2.",
+    citations=[citations["Milanese2019-gw"]],
+    input_descriptions={"motus_table": "The path to a precomputed merged mOTU table."},
+    parameter_descriptions={"ncbi_taxonomy": "Use NCBI taxonomy instead of mOTU."},
+    output_descriptions={"table": "The feature table with counts of marker genes in samples.",
+                         "taxonomy": "The taxonomy."}
+)
+
diff --git a/q2_motus/tests/data/motus-merged-abundance-1.tsv b/q2_motus/tests/data/motus-merged-abundance-1.tsv
@@ -0,0 +1,14 @@
+# motus version 3.0.3 | merge 3.0.3 | info merged profiles: # git tag version 3.0.3 |  motus version 3.0.3 | map_tax 3.0.3 | gene database: nr3.0.3 | calc_mgc 3.0.3 -y insert.scaled_counts -l 75 | calc_motu 3.0.3 -k mOTU -C no_CAMI -g 3 -c | taxonomy: ref_mOTU_3.0.3 meta_mOTU_3.0.3 
+# call: python /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/vbezshapkin/conda-envs/qiime2/bin/motus merge -i A.motus,B.motus -o paired-end.motus
+#mOTU	consensus_taxonomy	sampleA	sampleB
+ref_mOTU_v3_00095	k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli	1	0
+ref_mOTU_v3_00096	k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__ Citrobacter sp. [Citrobacter amalonaticus/Citrobacter braakii/Citrobacter freundii/Citrobacter pasteurii/Citrobacter portucalensis/Citrobacter sp. A1/Citrobacter sp. A316/Citrobacter sp. AATXQ/Citrobacter sp. AATXR/Citrobacter sp. BIDMC107/Citrobacter sp. BIDMC108/Citrobacter sp. CFSAN044567/Citrobacter sp. FDAARGOS_156/Citrobacter sp. KTE151/Citrobacter sp. KTE30/Citrobacter sp. KTE32/Citrobacter sp. L17/Citrobacter sp. MGH100/Citrobacter sp. MGH103/Citrobacter sp. MGH104/Citrobacter sp. MGH105/Citrobacter sp. MGH109/Citrobacter sp. MGH110/Citrobacter sp. MGH99/Citrobacter werkmanii/Citrobacter youngae/Enterobacter cloacae/Enterobacter sp. GN02600/Escherichia coli/Salmonella enterica]	1	0
+ref_mOTU_v3_00855	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis	0	1
+ref_mOTU_v3_02367	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides dorei/vulgatus [Bacteroidia bacterium UC5.1-2G11/Candidatus Gastranaerophilales bacterium HUM_8/Bacteroides dorei/Bacteroides sp. 3_1_33FAA/Bacteroides sp. 4_3_47FAA/Bacteroides sp. 9_1_42FAA/Bacteroides sp. 3_1_40A/Bacteroides vulgatus]	0	1
+ref_mOTU_v3_03592	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp. CAG:344	1	0
+ref_mOTU_v3_03928	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales fam. incertae sedis|g__Intestinimonas|s__Intestinimonas butyriciproducens [Intestinimonas butyriciproducens/uncultured Clostridium sp.]	0	1
+ref_mOTU_v3_04716	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans [Ruthenibacterium lactatiformans/Ruminococcaceae bacterium cv2/Subdoligranulum sp. 4_3_54A2FAA]	1	1
+ref_mOTU_v3_05238	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Flavonifractor|s__Flavonifractor plautii [Clostridia bacterium UC5.1-2H11/Flavonifractor plautii/Lachnospiraceae bacterium 7_1_58FAA]	1	0
+meta_mOTU_v3_12805	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia species incertae sedis	1	0
+ext_mOTU_v3_26730	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia species incertae sedis	1	0
+unassigned	unassigned	1	1
diff --git a/q2_motus/tests/data/motus-merged-abundance-2.tsv b/q2_motus/tests/data/motus-merged-abundance-2.tsv
@@ -0,0 +1,14 @@
+# motus version 3.0.3 | merge 3.0.3 | info merged profiles: # git tag version 3.0.3 |  motus version 3.0.3 | map_tax 3.0.3 | gene database: nr3.0.3 | calc_mgc 3.0.3 -y insert.scaled_counts -l 75 | calc_motu 3.0.3 -k mOTU -C no_CAMI -g 3 -c | taxonomy: ref_mOTU_3.0.3 meta_mOTU_3.0.3 
+# call: python /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/vbezshapkin/conda-envs/qiime2/bin/motus merge -i A.motus,B.motus -o paired-end.motus
+#mOTU	consensus_taxonomy
+ref_mOTU_v3_00095	k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli
+ref_mOTU_v3_00096	k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__ Citrobacter sp. [Citrobacter amalonaticus/Citrobacter braakii/Citrobacter freundii/Citrobacter pasteurii/Citrobacter portucalensis/Citrobacter sp. A1/Citrobacter sp. A316/Citrobacter sp. AATXQ/Citrobacter sp. AATXR/Citrobacter sp. BIDMC107/Citrobacter sp. BIDMC108/Citrobacter sp. CFSAN044567/Citrobacter sp. FDAARGOS_156/Citrobacter sp. KTE151/Citrobacter sp. KTE30/Citrobacter sp. KTE32/Citrobacter sp. L17/Citrobacter sp. MGH100/Citrobacter sp. MGH103/Citrobacter sp. MGH104/Citrobacter sp. MGH105/Citrobacter sp. MGH109/Citrobacter sp. MGH110/Citrobacter sp. MGH99/Citrobacter werkmanii/Citrobacter youngae/Enterobacter cloacae/Enterobacter sp. GN02600/Escherichia coli/Salmonella enterica]
+ref_mOTU_v3_00855	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis
+ref_mOTU_v3_02367	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides dorei/vulgatus [Bacteroidia bacterium UC5.1-2G11/Candidatus Gastranaerophilales bacterium HUM_8/Bacteroides dorei/Bacteroides sp. 3_1_33FAA/Bacteroides sp. 4_3_47FAA/Bacteroides sp. 9_1_42FAA/Bacteroides sp. 3_1_40A/Bacteroides vulgatus]
+ref_mOTU_v3_03592	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp. CAG:344
+ref_mOTU_v3_03928	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales fam. incertae sedis|g__Intestinimonas|s__Intestinimonas butyriciproducens [Intestinimonas butyriciproducens/uncultured Clostridium sp.]
+ref_mOTU_v3_04716	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans [Ruthenibacterium lactatiformans/Ruminococcaceae bacterium cv2/Subdoligranulum sp. 4_3_54A2FAA]
+ref_mOTU_v3_05238	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Flavonifractor|s__Flavonifractor plautii [Clostridia bacterium UC5.1-2H11/Flavonifractor plautii/Lachnospiraceae bacterium 7_1_58FAA]
+meta_mOTU_v3_12805	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia species incertae sedis
+ext_mOTU_v3_26730	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia species incertae sedis
+unassigned	unassigned
diff --git a/q2_motus/tests/data/motus-merged-abundance-3.tsv b/q2_motus/tests/data/motus-merged-abundance-3.tsv
@@ -0,0 +1,14 @@
+# motus version 3.0.3 | merge 3.0.3 | info merged profiles: # git tag version 3.0.3 |  motus version 3.0.3 | map_tax 3.0.3 | gene database: nr3.0.3 | calc_mgc 3.0.3 -y insert.scaled_counts -l 75 | calc_motu 3.0.3 -k mOTU -C no_CAMI -g 3 -c | taxonomy: ref_mOTU_3.0.3 meta_mOTU_3.0.3 
+# call: python /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/vbezshapkin/conda-envs/qiime2/bin/motus merge -i A.motus,B.motus -o paired-end.motus
+#mOTU	consensus_taxonomy	sampleA	sampleB
+ref_mOTU_v3_00095	k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli	1.0	0.0
+ref_mOTU_v3_00096	k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__ Citrobacter sp. [Citrobacter amalonaticus/Citrobacter braakii/Citrobacter freundii/Citrobacter pasteurii/Citrobacter portucalensis/Citrobacter sp. A1/Citrobacter sp. A316/Citrobacter sp. AATXQ/Citrobacter sp. AATXR/Citrobacter sp. BIDMC107/Citrobacter sp. BIDMC108/Citrobacter sp. CFSAN044567/Citrobacter sp. FDAARGOS_156/Citrobacter sp. KTE151/Citrobacter sp. KTE30/Citrobacter sp. KTE32/Citrobacter sp. L17/Citrobacter sp. MGH100/Citrobacter sp. MGH103/Citrobacter sp. MGH104/Citrobacter sp. MGH105/Citrobacter sp. MGH109/Citrobacter sp. MGH110/Citrobacter sp. MGH99/Citrobacter werkmanii/Citrobacter youngae/Enterobacter cloacae/Enterobacter sp. GN02600/Escherichia coli/Salmonella enterica]	1.0	0.0
+ref_mOTU_v3_00855	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis	0.0	1.0
+ref_mOTU_v3_02367	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides dorei/vulgatus [Bacteroidia bacterium UC5.1-2G11/Candidatus Gastranaerophilales bacterium HUM_8/Bacteroides dorei/Bacteroides sp. 3_1_33FAA/Bacteroides sp. 4_3_47FAA/Bacteroides sp. 9_1_42FAA/Bacteroides sp. 3_1_40A/Bacteroides vulgatus]	0.0	1.0
+ref_mOTU_v3_03592	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp. CAG:344	1.0	0.0
+ref_mOTU_v3_03928	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales fam. incertae sedis|g__Intestinimonas|s__Intestinimonas butyriciproducens [Intestinimonas butyriciproducens/uncultured Clostridium sp.]	0.0	1.0
+ref_mOTU_v3_04716	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans [Ruthenibacterium lactatiformans/Ruminococcaceae bacterium cv2/Subdoligranulum sp. 4_3_54A2FAA]	1.0	1.0
+ref_mOTU_v3_05238	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Flavonifractor|s__Flavonifractor plautii [Clostridia bacterium UC5.1-2H11/Flavonifractor plautii/Lachnospiraceae bacterium 7_1_58FAA]	1.0	0.0
+meta_mOTU_v3_12805	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia species incertae sedis	1.0	0.0
+ext_mOTU_v3_26730	k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia species incertae sedis	1.0	0.0
+unassigned	unassigned	1.0	1.0