# Copyright (c) 2016-2017, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from ..plugin_setup import plugin
from ..sample_data import SampleData
from . import (SingleLanePerSampleSingleEndFastqDirFmt,
SingleLanePerSamplePairedEndFastqDirFmt)
SequencesWithQuality = SemanticType(
'SequencesWithQuality', variant_of=SampleData.field['type'])
PairedEndSequencesWithQuality = SemanticType(
'PairedEndSequencesWithQuality', variant_of=SampleData.field['type'])
plugin.register_semantic_types(SequencesWithQuality,
PairedEndSequencesWithQuality)
plugin.register_semantic_type_to_format(
SampleData[SequencesWithQuality],
artifact_format=SingleLanePerSampleSingleEndFastqDirFmt
)
plugin.register_semantic_type_to_format(
SampleData[PairedEndSequencesWithQuality],
artifact_format=SingleLanePerSamplePairedEndFastqDirFmt
)
from qiime2.plugin import SemanticType, model
from q2_types.sample_data import SampleData
SongbirdStats = SemanticType('SongbirdStats',
variant_of=SampleData.field['type'])
class SongbirdStatsFormat(model.TextFileFormat):
def validate(*args):
pass
SongbirdStatsDirFmt = model.SingleFileDirectoryFormat('SongbirdStatsDirFmt',
'stats.tsv',
SongbirdStatsFormat)
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2018, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType, model
from q2_types.sample_data import SampleData
DADA2Stats = SemanticType('DADA2Stats', variant_of=SampleData.field['type'])
class DADA2StatsFormat(model.TextFileFormat):
def validate(*args):
pass
DADA2StatsDirFmt = model.SingleFileDirectoryFormat('DADA2StatsDirFmt',
'stats.tsv',
DADA2StatsFormat)
from qiime2.plugin import SemanticType, model
from q2_types.sample_data import SampleData
StrayPosterior = SemanticType('StrayPosterior',
variant_of=SampleData.field['type'])
class StrayPosteriorFormat(model.TextFileFormat):
def validate(*args):
pass
StrayPosteriorDirFmt = model.SingleFileDirectoryFormat('StrayPosteriorDirFmt',
'posterior.tsv',
StrayPosteriorFormat)
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2017, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
QualityFilterStats = SemanticType('QualityFilterStats')
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
DeblurStats = SemanticType('DeblurStats')
from qiime2.plugin import SemanticType, model
from q2_types.feature_data import FeatureData
Conditional = SemanticType('Conditional', variant_of=FeatureData.field['type'])
class ConditionalFormat(model.TextFileFormat):
def validate(*args):
pass
ConditionalDirFmt = model.SingleFileDirectoryFormat('ConditionalDirFmt',
'conditionals.tsv',
ConditionalFormat)
from qiime2.plugin import SemanticType
from q2_types.feature_data import FeatureData
from q2_types.feature_table import FeatureTable
TaxIdLineage = SemanticType('TaxIdLineage')
LinkedSpeciesPeptide = SemanticType('LinkedSpeciesPeptide')
SequenceNames = SemanticType('SequenceNames')
ProteinSequence = SemanticType('ProteinSequence',
variant_of=FeatureData.field['type'])
EnrichedPeptide = SemanticType('EnrichedPeptide')
DeconvolutedSpecies = SemanticType('DeconvolutedSpecies',
variant_of=FeatureTable.field['content'])
SpeciesAssignMap = SemanticType('SpeciesAssignMap')
import numpy as np
from q2_classo.CLasso import *
from qiime2.plugin import (SemanticType, Plugin, Int, Float, Range, Metadata,
Str, Bool, Choices, MetadataColumn, Categorical,
List, Citations, TypeMatch, Numeric)
from q2_types.feature_table import FeatureTable, Composition
from q2_types.feature_data import FeatureData
Beta_type = SemanticType(
'Beta_type'
) # array of size Npath x d with the solution beta for each lambda on each row
Sigma_type = SemanticType(
'Sigma_type'
) # array of size Npath with the solution sigma for each lambda when the formulation of the problem is R2 or R4
Lambda_type = SemanticType(
'Lambda_type'
) # array of size Npath with the lambdas (real lambdas, not divided by lambda_max) for which the solution is computed
Method_type = SemanticType(
'Method_type'
) # name of the numerical method that has been used. It can be 'Path-Alg', 'P-PDS' , 'PF-PDS' or 'DR'
Formulation_type = SemanticType(
'Formulation_type') # can be 'R1' ; 'R2' ; 'R3' ; 'R4' ; 'C1' ; 'C2'
Time_type = SemanticType('Time_type') # running time of this action
Path_type = SemanticType('Path_type',
field_names=[
'betas', 'sigmas', 'lambdas', 'method',
'formulation', 'time'
],
field_members={
'betas': Beta_type,
# ----------------------------------------------------------------------------
# Copyright (c) 2018-2020, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
# Technically there is a bit more to this, for instance the ref sequences may
# or may not be present in an index, or may be the only thing in an index,
# but let's not worry about that just yet.
Bowtie2Index = SemanticType('Bowtie2Index')
from qiime2.plugin import SemanticType
from q2_types.tree import Phylogeny
Chain = SemanticType('Chain', field_names='posterior')
BEAST = SemanticType('BEAST', variant_of=Chain.field['posterior'])
MCC = SemanticType('MCC', variant_of=Phylogeny.field['type'])
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2020, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from ..plugin_setup import plugin
from . import AlphaDiversityDirectoryFormat
SampleData = SemanticType('SampleData', field_names='type')
AlphaDiversity = SemanticType('AlphaDiversity',
variant_of=SampleData.field['type'])
plugin.register_semantic_types(SampleData, AlphaDiversity)
plugin.register_semantic_type_to_format(
SampleData[AlphaDiversity],
artifact_format=AlphaDiversityDirectoryFormat
)
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2019, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from ..plugin_setup import plugin
from . import OrdinationDirectoryFormat
PCoAResults = SemanticType('PCoAResults')
plugin.register_semantic_types(PCoAResults)
plugin.register_semantic_type_to_format(
PCoAResults, artifact_format=OrdinationDirectoryFormat)
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2018, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
UchimeStats = SemanticType('UchimeStats')
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2017, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
NinjaOpsDB = SemanticType('NinjaOpsDB')
citations = Citations.load('citations.bib', package='q2_sample_classifier')
plugin = Plugin(
name='sample-classifier',
version=q2_sample_classifier.__version__,
website="https://github.com/qiime2/q2-sample-classifier",
package='q2_sample_classifier',
description=(
'This QIIME 2 plugin supports methods for supervised classification '
'and regression of sample metadata, and other supervised machine '
'learning methods.'),
short_description=(
'Plugin for machine learning prediction of sample metadata.'),
citations=[citations['Bokulich306167']])
BooleanSeries = SemanticType('BooleanSeries',
variant_of=SampleData.field['type'])
class BooleanSeriesFormat(model.TextFileFormat):
def sniff(self):
with self.open() as fh:
line = fh.readline()
for line, _ in zip(fh, range(5)):
cells = line.strip().split('\t')
if len(cells) != 2 or str(cells[1]) not in ('True', 'False'):
return False
return True
BooleanSeriesDirectoryFormat = model.SingleFileDirectoryFormat(
'BooleanSeriesDirectoryFormat', 'outliers.tsv', BooleanSeriesFormat)
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from ..plugin_setup import plugin
from . import BIOMV210DirFmt
FeatureTable = SemanticType('FeatureTable', field_names='content')
Frequency = SemanticType('Frequency', variant_of=FeatureTable.field['content'])
RelativeFrequency = SemanticType('RelativeFrequency',
variant_of=FeatureTable.field['content'])
PresenceAbsence = SemanticType('PresenceAbsence',
variant_of=FeatureTable.field['content'])
Composition = SemanticType('Composition',
variant_of=FeatureTable.field['content'])
Balance = SemanticType('Balance', variant_of=FeatureTable.field['content'])
PercentileNormalized = SemanticType('PercentileNormalized',
variant_of=FeatureTable.field['content'])
# ----------------------------------------------------------------------------
# Copyright (c) 2017-2018, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from q2_types.sample_data import SampleData
FirstDifferences = SemanticType('FirstDifferences',
variant_of=SampleData.field['type'])
# ----------------------------------------------------------------------------
# Copyright (c) 2017-2019, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from q2_types.sample_data import SampleData
from q2_types.feature_data import FeatureData
ClassifierPredictions = SemanticType('ClassifierPredictions',
variant_of=SampleData.field['type'])
RegressorPredictions = SemanticType('RegressorPredictions',
variant_of=SampleData.field['type'])
SampleEstimator = SemanticType('SampleEstimator', field_names='type')
Classifier = SemanticType('Classifier',
variant_of=SampleEstimator.field['type'])
Regressor = SemanticType('Regressor', variant_of=SampleEstimator.field['type'])
BooleanSeries = SemanticType('BooleanSeries',
variant_of=SampleData.field['type'])
Importance = SemanticType('Importance', variant_of=FeatureData.field['type'])
Probabilities = SemanticType('Probabilities',
variant_of=SampleData.field['type'])
# Copyright (c) 2016-2018, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from ..plugin_setup import plugin
from . import (TSVTaxonomyDirectoryFormat, DNASequencesDirectoryFormat,
PairedDNASequencesDirectoryFormat,
AlignedDNASequencesDirectoryFormat)
FeatureData = SemanticType('FeatureData', field_names='type')
Taxonomy = SemanticType('Taxonomy', variant_of=FeatureData.field['type'])
Sequence = SemanticType('Sequence', variant_of=FeatureData.field['type'])
PairedEndSequence = SemanticType('PairedEndSequence',
variant_of=FeatureData.field['type'])
AlignedSequence = SemanticType('AlignedSequence',
variant_of=FeatureData.field['type'])
plugin.register_semantic_types(FeatureData, Taxonomy, Sequence,
PairedEndSequence, AlignedSequence)
plugin.register_semantic_type_to_format(
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2019, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
# TODO: migrate these to q2-types someday
RawSequences = SemanticType('RawSequences')
EMPSingleEndSequences = SemanticType('EMPSingleEndSequences')
EMPPairedEndSequences = SemanticType('EMPPairedEndSequences')
ErrorCorrectionDetails = SemanticType('ErrorCorrectionDetails')
# ----------------------------------------------------------------------------
# Copyright (c) 2017-2018, Ben Kaehler.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
PrecalculatedNearestNeighbors = SemanticType('PrecalculatedNearestNeighbors')
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2020, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from ..plugin_setup import plugin
from . import (MultiplexedSingleEndBarcodeInSequenceDirFmt,
MultiplexedPairedEndBarcodeInSequenceDirFmt)
MultiplexedSingleEndBarcodeInSequence = \
SemanticType('MultiplexedSingleEndBarcodeInSequence')
MultiplexedPairedEndBarcodeInSequence = \
SemanticType('MultiplexedPairedEndBarcodeInSequence')
plugin.register_semantic_types(MultiplexedSingleEndBarcodeInSequence,
MultiplexedPairedEndBarcodeInSequence)
plugin.register_semantic_type_to_format(
MultiplexedSingleEndBarcodeInSequence,
artifact_format=MultiplexedSingleEndBarcodeInSequenceDirFmt)
plugin.register_semantic_type_to_format(
MultiplexedPairedEndBarcodeInSequence,
artifact_format=MultiplexedPairedEndBarcodeInSequenceDirFmt,
)
# ----------------------------------------------------------------------------
# Copyright (c) 2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from q2_types.feature_data import FeatureData
SILVATaxonomy = SemanticType('SILVATaxonomy',
variant_of=FeatureData.field['type'])
SILVATaxidMap = SemanticType('SILVATaxidMap',
variant_of=FeatureData.field['type'])
RNASequence = SemanticType('RNASequence', variant_of=FeatureData.field['type'])
# ----------------------------------------------------------------------------
# Copyright (c) 2020, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType, model
EchoOutput = SemanticType('EchoOutput')
class EchoOutputFmt(model.TextFileFormat):
def validate(self, *args):
pass
EchoOutputDirFmt = model.SingleFileDirectoryFormat('EchoOutputDirFmt',
'echo.txt', EchoOutputFmt)
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from ..plugin_setup import plugin
from . import DistanceMatrixDirectoryFormat
DistanceMatrix = SemanticType('DistanceMatrix')
plugin.register_semantic_types(DistanceMatrix)
plugin.register_semantic_type_to_format(
DistanceMatrix, artifact_format=DistanceMatrixDirectoryFormat)
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from ..plugin_setup import plugin
from . import (TSVTaxonomyDirectoryFormat, DNASequencesDirectoryFormat,
PairedDNASequencesDirectoryFormat,
AlignedDNASequencesDirectoryFormat,
DifferentialDirectoryFormat, ProteinSequencesDirectoryFormat,
AlignedProteinSequencesDirectoryFormat,
RNASequencesDirectoryFormat, AlignedRNASequencesDirectoryFormat,
PairedRNASequencesDirectoryFormat)
FeatureData = SemanticType('FeatureData', field_names='type')
Taxonomy = SemanticType('Taxonomy', variant_of=FeatureData.field['type'])
Sequence = SemanticType('Sequence', variant_of=FeatureData.field['type'])
RNASequence = SemanticType('RNASequence', variant_of=FeatureData.field['type'])
PairedEndSequence = SemanticType('PairedEndSequence',
variant_of=FeatureData.field['type'])
PairedEndRNASequence = SemanticType('PairedEndRNASequence',
variant_of=FeatureData.field['type'])
AlignedSequence = SemanticType('AlignedSequence',
variant_of=FeatureData.field['type'])
# ----------------------------------------------------------------------------
# Copyright (c) 2020, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
from q2_types.sample_data import SampleData
Coordinates = SemanticType('Coordinates', variant_of=SampleData.field['type'])
QuadTree = SemanticType('QuadTree', variant_of=SampleData.field['type'])
from qiime2.plugin import SemanticType, model
from q2_types.feature_data import FeatureData
Factors = SemanticType('Factors', variant_of=FeatureData.field['type'])
class FactorsFormat(model.TextFileFormat):
# Update with required formatting
def validate(*args):
pass
FactorsDirFmt = model.SingleFileDirectoryFormat('FactorsDirFmt', 'factors.tsv',
FactorsFormat)
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2020, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import SemanticType
Placements = SemanticType('Placements')
SeppReferenceDatabase = SemanticType('SeppReferenceDatabase')
