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# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, 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.
# ----------------------------------------------------------------------------
import importlib
import qiime2.plugin
from qiime2.plugin import Citations
from q2_types.feature_data import FeatureData, Sequence, Taxonomy
from q2_types.feature_table import FeatureTable, Frequency
from q2_types.tree import Phylogeny, Rooted
import q2_fragment_insertion
from q2_fragment_insertion._type import Placements, SeppReferenceDatabase
from q2_fragment_insertion._format import (
PlacementsFormat, PlacementsDirFmt, SeppReferenceDirFmt, RAxMLinfoFormat)
citations = Citations.load('citations.bib', package='q2_fragment_insertion')
plugin = qiime2.plugin.Plugin(
name='fragment-insertion',
version=q2_fragment_insertion.__version__,
website='https://github.com/qiime2/q2-fragment-insertion',
short_description='Plugin for extending phylogenies.',
package='q2_fragment_insertion',
user_support_text='https://github.com/qiime2/q2-fragment-insertion/issues',
citations=citations,
)
plugin.methods.register_function(
function=q2_fragment_insertion.sepp,
inputs={
'representative_sequences': FeatureData[Sequence],
'reference_database': SeppReferenceDatabase,
},
parameters={
'threads': qiime2.plugin.Threads,
'alignment_subset_size': qiime2.plugin.Int,
'placement_subset_size': qiime2.plugin.Int,
'debug': qiime2.plugin.Bool,
},
outputs=[
('tree', Phylogeny[Rooted]),
('placements', Placements),
],
input_descriptions={
'representative_sequences': 'The sequences to insert into the '
'reference tree.',
'reference_database': 'The reference database to insert the '
'representative sequences into.',
},
parameter_descriptions={
'threads': 'The number of threads to use. Pass 0 to use one per '
'available core.',
'alignment_subset_size': 'Each placement subset is further broken '
'into subsets of at most these many '
'sequences and a separate HMM is trained on '
'each subset.',
'placement_subset_size': 'The tree is divided into subsets such that '
'each subset includes at most these many '
'subsets. The placement step places the '
'fragment on only one subset, determined '
'based on alignment scores. Further '
'reading: https://github.com/smirarab/sepp/'
'blob/master/tutorial/sepp-tutorial.md#sample'
'-datasets-default-parameters.',
'debug': 'Collect additional run information to STDOUT for debugging. '
'Temporary directories will not be removed if run fails.'
},
output_descriptions={
'tree': 'The tree with inserted feature data.',
'placements': 'Information about the feature placements within the '
'reference tree.',
},
name='Insert fragment sequences using SEPP into reference phylogenies.',
description='Perform fragment insertion of sequences using the SEPP '
'algorithm.',
)
plugin.methods.register_function(
function=q2_fragment_insertion.classify_otus_experimental,
inputs={
'representative_sequences': FeatureData[Sequence],
'tree': Phylogeny[Rooted],
'reference_taxonomy': FeatureData[Taxonomy],
},
input_descriptions={
'representative_sequences': 'The sequences used for a \'sepp\' run '
'to produce the \'tree\'.',
'tree': 'The tree resulting from inserting fragments into a reference '
'phylogeny, i.e. the output of function \'sepp\'',
'reference_taxonomy': 'Reference taxonomic table that maps every '
'OTU-ID into a taxonomic lineage string.',
},
parameters={},
parameter_descriptions={},
outputs=[
('classification', FeatureData[Taxonomy]),
],
output_descriptions={
'classification': 'Taxonomic lineages for inserted fragments.',
},
name='Experimental: Obtain taxonomic lineages, by finding closest OTU in '
'reference phylogeny.',
description='Experimental: Use the resulting tree from \'sepp\' and find '
'closest OTU-ID for every inserted fragment. Then, look up '
'the reference lineage string in the reference taxonomy.',
)
plugin.methods.register_function(
function=q2_fragment_insertion.filter_features,
inputs={
'table': FeatureTable[Frequency],
'tree': Phylogeny[Rooted],
},
input_descriptions={
'table': 'A feature-table which needs to filtered down to those '
'fragments that are contained in the tree, e.g. result of a '
'Deblur or DADA2 run.',
'tree': 'The tree resulting from inserting fragments into a reference '
'phylogeny, i.e. the output of function \'sepp\'',
},
parameters={},
parameter_descriptions={},
outputs=[
('filtered_table', FeatureTable[Frequency]),
('removed_table', FeatureTable[Frequency]),
],
output_descriptions={
'filtered_table': 'The input table minus those fragments that were '
'not part of the tree. This feature-table can be '
'used for downstream analyses like phylogenetic '
'alpha- or beta- diversity computation.',
'removed_table': 'Those fragments that got removed from the input '
'table, because they were not part of the tree. This '
'table is mainly used for quality control, e.g. to '
'inspect the ratio of removed reads per sample from '
'the input table. You can ignore this table for '
'downstream analyses.',
},
name='Filter fragments in tree from table.',
description='Filters fragments not inserted into a phylogenetic tree from '
'a feature-table. Some fragments computed by e.g. Deblur or '
'DADA2 are too remote to get inserted by SEPP into a '
'reference phylogeny. To be able to use the feature-table for '
'downstream analyses like computing Faith\'s PD or UniFrac, '
'the feature-table must be cleared of fragments that are not '
'part of the phylogenetic tree, because their path length can '
'otherwise not be determined. Typically, the number of '
'rejected fragments is low (<= 10), but it might be worth to '
'inspect the ratio of rea' 'ds assigned to those rejected '
'fragments.',
)
# TODO: rough in method to merge database components
# TODO: rough in method to destructure database components
importlib.import_module('q2_fragment_insertion._transformer')
plugin.register_formats(PlacementsFormat, PlacementsDirFmt, RAxMLinfoFormat,
SeppReferenceDirFmt)
plugin.register_semantic_types(Placements, SeppReferenceDatabase)
plugin.register_semantic_type_to_format(Placements,
artifact_format=PlacementsDirFmt)
plugin.register_semantic_type_to_format(SeppReferenceDatabase,
artifact_format=SeppReferenceDirFmt)
|
