# 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')