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REF: feature_table
1 parent f561977 commit d1cb02d

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lines changed

‎q2_types/__init__.py

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__version__ = get_versions()['version']
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del get_versions
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importlib.import_module('q2_types.feature_table')
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importlib.import_module('q2_types.tree')
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importlib.import_module('q2_types.ordination')
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importlib.import_module('q2_types.sample_data')

‎q2_types/citations.bib

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@article{mcdonald2012biological,
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title={The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome},
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author={McDonald, Daniel and Clemente, Jose C and Kuczynski, Justin and Rideout, Jai Ram and Stombaugh, Jesse and Wendel, Doug and Wilke, Andreas and Huse, Susan and Hufnagle, John and Meyer, Folker and Knight, Rob and Caporaso, J Gregory},
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journal={GigaScience},
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volume={1},
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number={1},
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pages={7},
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year={2012},
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publisher={BioMed Central},
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doi={10.1186/2047-217X-1-7}
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}
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@InProceedings{ mckinney-proc-scipy-2010,
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author = { Wes McKinney },
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title = { Data Structures for Statistical Computing in Python },

‎q2_types/feature_table/__init__.py

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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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import importlib
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from ._format import (BIOMV100Format, BIOMV210Format, BIOMV100DirFmt,
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BIOMV210DirFmt)
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from ._type import (FeatureTable, Frequency, RelativeFrequency,
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PresenceAbsence, Composition, Balance,
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PercentileNormalized, Design)
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from ._formats import (BIOMV100Format, BIOMV210Format, BIOMV100DirFmt,
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BIOMV210DirFmt)
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from ._types import (FeatureTable, Frequency, RelativeFrequency,
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PresenceAbsence, Composition, Balance,
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PercentileNormalized, Design)
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__all__ = ['BIOMV100Format', 'BIOMV100DirFmt', 'FeatureTable', 'Frequency',
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'RelativeFrequency', 'PresenceAbsence', 'BIOMV210Format',
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'BIOMV210DirFmt', 'Composition', 'Balance', 'PercentileNormalized',
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'Design']
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importlib.import_module('q2_types.feature_table._transformer')

‎q2_types/feature_table/_type.py ‎q2_types/feature_table/_deferred_setup/__init__.py

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@@ -6,34 +6,24 @@
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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from qiime2.plugin import SemanticType
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import importlib
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from ..plugin_setup import plugin
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from . import BIOMV210DirFmt
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import biom
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from qiime2.plugin import Citations
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FeatureTable = SemanticType('FeatureTable', field_names='content')
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from .. import (BIOMV100Format, BIOMV210Format, BIOMV100DirFmt,
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BIOMV210DirFmt, FeatureTable, Frequency, RelativeFrequency,
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PresenceAbsence, Composition, Balance,
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PercentileNormalized, Design)
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Frequency = SemanticType('Frequency', variant_of=FeatureTable.field['content'])
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from ...plugin_setup import plugin
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RelativeFrequency = SemanticType('RelativeFrequency',
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variant_of=FeatureTable.field['content'])
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citations = Citations.load('citations.bib', package='q2_types.feature_table')
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PresenceAbsence = SemanticType('PresenceAbsence',
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variant_of=FeatureTable.field['content'])
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Composition = SemanticType('Composition',
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variant_of=FeatureTable.field['content'])
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Balance = SemanticType('Balance',
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variant_of=FeatureTable.field['content'])
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PercentileNormalized = SemanticType('PercentileNormalized',
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variant_of=FeatureTable.field['content'])
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# Design is the type of design matrices for linear regressions that have
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# been transformed/coded.
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Design = SemanticType('Design', variant_of=FeatureTable.field['content'])
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plugin.register_views(BIOMV100Format, BIOMV210Format, BIOMV100DirFmt,
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BIOMV210DirFmt, biom.Table,
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citations=[citations['mcdonald2012biological']])
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plugin.register_semantic_types(FeatureTable, Frequency, RelativeFrequency,
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PresenceAbsence, Balance, Composition,
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FeatureTable[Design],
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directory_format=BIOMV210DirFmt
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)
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importlib.import_module('._transformers', __name__)

‎q2_types/feature_table/_transformer.py ‎q2_types/feature_table/_deferred_setup/_transformers.py

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import pandas as pd
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import qiime2
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from . import BIOMV100Format, BIOMV210Format
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from ..plugin_setup import plugin
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from .. import BIOMV100Format, BIOMV210Format
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from ...plugin_setup import plugin
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# NOTE: In the readers and writers for BIOM v1 and v2 below, metadata must be
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# ignored on both axes because BIOM v1 and v2 are incompatible with certain

‎q2_types/feature_table/_format.py ‎q2_types/feature_table/_formats.py

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# ----------------------------------------------------------------------------
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import ijson
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import h5py
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import biom
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import qiime2.plugin.model as model
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from ..plugin_setup import plugin, citations
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class BIOMV100Format(model.TextFileFormat):
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top_level_keys = {
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BIOMV210DirFmt = model.SingleFileDirectoryFormat('BIOMV210DirFmt',
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'feature-table.biom',
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BIOMV210Format)
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plugin.register_views(BIOMV100Format, BIOMV210Format, BIOMV100DirFmt,
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BIOMV210DirFmt, biom.Table,
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citations=[citations['mcdonald2012biological']])

‎q2_types/feature_table/_types.py

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# ----------------------------------------------------------------------------
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# Copyright (c) 2016-2023, QIIME 2 development team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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from qiime2.plugin import SemanticType
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FeatureTable = SemanticType('FeatureTable', field_names='content')
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Frequency = SemanticType('Frequency', variant_of=FeatureTable.field['content'])
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RelativeFrequency = SemanticType('RelativeFrequency',
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variant_of=FeatureTable.field['content'])
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PresenceAbsence = SemanticType('PresenceAbsence',
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variant_of=FeatureTable.field['content'])
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Composition = SemanticType('Composition',
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variant_of=FeatureTable.field['content'])
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Balance = SemanticType('Balance',
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variant_of=FeatureTable.field['content'])
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PercentileNormalized = SemanticType('PercentileNormalized',
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variant_of=FeatureTable.field['content'])
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# Design is the type of design matrices for linear regressions that have
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# been transformed/coded.
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Design = SemanticType('Design', variant_of=FeatureTable.field['content'])

‎q2_types/feature_table/citations.bib

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@article{mcdonald2012biological,
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title={The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome},
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author={McDonald, Daniel and Clemente, Jose C and Kuczynski, Justin and Rideout, Jai Ram and Stombaugh, Jesse and Wendel, Doug and Wilke, Andreas and Huse, Susan and Hufnagle, John and Meyer, Folker and Knight, Rob and Caporaso, J Gregory},
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journal={GigaScience},
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volume={1},
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number={1},
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pages={7},
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year={2012},
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publisher={BioMed Central},
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doi={10.1186/2047-217X-1-7}
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}

‎q2_types/feature_table/tests/test_format.py ‎q2_types/feature_table/tests/test_formats.py

File renamed without changes.

‎q2_types/feature_table/tests/test_transformer.py ‎q2_types/feature_table/tests/test_transformers.py

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import biom
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import pandas as pd
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import qiime2
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from numpy.testing import assert_array_equal
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from pandas.testing import assert_frame_equal
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from q2_types.feature_table import BIOMV100Format, BIOMV210Format
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import qiime2
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from qiime2.plugin.testing import TestPluginBase
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from q2_types.feature_table._transformer import (_parse_biom_table_v100,
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_parse_biom_table_v210,
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_table_to_dataframe,
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_table_to_metadata)
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from q2_types.feature_table import BIOMV100Format, BIOMV210Format
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from q2_types.feature_table._deferred_setup._transformers import (
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_parse_biom_table_v100, _parse_biom_table_v210, _table_to_dataframe,
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_table_to_metadata)
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class TestTransformers(TestPluginBase):

‎q2_types/feature_table/tests/test_type.py ‎q2_types/feature_table/tests/test_types.py

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import unittest
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from qiime2.plugin.testing import TestPluginBase
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from q2_types.feature_table import (FeatureTable, Frequency,
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RelativeFrequency, PercentileNormalized,
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Composition, Balance,
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PresenceAbsence, BIOMV210DirFmt, Design)
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from qiime2.plugin.testing import TestPluginBase
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class TestTypes(TestPluginBase):

‎q2_types/plugin_setup.py

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importlib.import_module('q2_types.feature_data._deferred_setup')
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importlib.import_module('q2_types.feature_data_mag._deferred_setup')
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importlib.import_module('q2_types.feature_map._deferred_setup')
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importlib.import_module('q2_types.feature_table._deferred_setup')
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importlib.import_module('q2_types.per_sample_sequences._deferred_setup')

‎setup.py

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'data/emp_multiplexed/*',
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'data/emp_multiplexed_single_end/*'],
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'q2_types.feature_map.tests': ['data/*'],
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'q2_types.feature_table': ['citations.bib'],
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'q2_types.feature_table.tests': ['data/*'],
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'q2_types.metadata.tests': ['data/*'],
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'q2_types.multiplexed_sequences.tests': [

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