diff --git a/CHANGELOG.md b/CHANGELOG.md index b7a7cf1..ad63c6c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,9 @@ # Greengenes2 changelog +## Version 2024.01 + +* Removed methods of bulk characterization which are resource, not user, oriented + ## Version 2022.12 * Added a method for collapsing by multifurcation in [#5](https://github.com/biocore/q2-greengenes2/pull/5) diff --git a/q2_gg2/plugin_setup.py b/q2_gg2/plugin_setup.py index 65cdbbf..ef093bc 100644 --- a/q2_gg2/plugin_setup.py +++ b/q2_gg2/plugin_setup.py @@ -131,82 +131,6 @@ ) -plugin.methods.register_function( - function=q2_gg2.bulk_sequence_v4_asv_assessment, - inputs={'phylogeny': Phylogeny[Rooted], - 'taxa': FeatureData[Taxonomy], - 'full_length_v4': FeatureData[Sequence], - 'sequences': FeatureData[Sequence]}, - parameters={'group': Int, - 'version': Str, - 'output_filename': Str}, - outputs=[('characterization', ASVAssessment)], - input_descriptions={ - 'phylogeny': 'The ID annotated phylogeny', - 'taxa': 'The taxa indexed by ID', - 'full_length_v4': 'The extracted V4 sequences from the backbone', - 'sequences': 'The full set of GG2 sequences'}, - parameter_descriptions={ - 'group': 'The hash group to process', - 'version': 'The database version to use', - 'output_filename': 'The file to write assessments too' - }, - output_descriptions={ - 'characterization': "This output is undefined"}, - name='Bulk ASV assessment', - description=("Check what full length records the ASV associates with " - "and members within its placement multifurcation"), - citations=[] -) - - -plugin.methods.register_function( - function=q2_gg2.bulk_clade_v4_asv_assessment, - inputs={'phylogeny': Phylogeny[Rooted], - 'taxa': FeatureData[Taxonomy], - 'full_length_v4': FeatureData[Sequence], - 'sequences': FeatureData[Sequence]}, - parameters={'group': Int, - 'version': Str, - 'output_filename': Str}, - outputs=[('characterization', CladeAssessment)], - input_descriptions={ - 'phylogeny': 'The ID annotated phylogeny', - 'taxa': 'The taxa indexed by ID', - 'full_length_v4': 'The extracted V4 sequences from the backbone', - 'sequences': 'The full set of GG2 sequences'}, - parameter_descriptions={ - 'group': 'The hash group to process', - 'version': 'The database version to use', - 'output_filename': 'The file to write assessments too' - }, - output_descriptions={'characterization': 'This output is undefined'}, - name='Bulk Clade ASV level assessment', - description=("Test whether the clade is uniquely represented by ASVs " - "and other summary information about the clade"), - citations=[] -) - - -plugin.methods.register_function( - function=q2_gg2.clade_lookup, - inputs={'taxonomy_as_tree': Phylogeny[Rooted]}, - parameters={'version': Str, - 'output_filename': Str}, - outputs=[('characterization', CladeAssessment)], - input_descriptions={ - 'taxonomy_as_tree': 'The taxonomy represented as a newick string'}, - parameter_descriptions={ - 'version': 'The database version to use', - 'output_filename': 'The file to write the lookup too' - }, - output_descriptions={'characterization': 'This output is undefined'}, - description=("Construct a taxonomy lookup suitable for a sqlite database"), - citations=[], - name='Construct a clade lookup' -) - - plugin.methods.register_function( function=q2_gg2.taxonomy_from_table, inputs={'reference_taxonomy': Phylogeny[Rooted],