ENH/DEP: add temporary action pending framework fix (#60)

caporaso-lab · Jul 29, 2020 · 6fe92ee · 6fe92ee
1 parent 66e6913
commit 6fe92ee
Show file tree

Hide file tree

Showing 2 changed files with 43 additions and 2 deletions.
diff --git a/genome_sampler/label_seqs.py b/genome_sampler/label_seqs.py
@@ -60,3 +60,10 @@ def label_seqs(seqs: pd.Series, delimiter: str,
     seqs.index = seqs.index.map(rename)
 
     return seqs
+
+
+def label_unaligned_seqs(seqs: pd.Series, delimiter: str,
+                         metadata: qiime2.Metadata = None, columns: str = None,
+                         missing_value: str = 'missing') \
+                   -> pd.Series:
+    return label_seqs(seqs, delimiter, metadata, columns, missing_value)
diff --git a/genome_sampler/plugin_setup.py b/genome_sampler/plugin_setup.py
@@ -45,7 +45,7 @@
 from genome_sampler.filter import filter_seqs
 from genome_sampler.combine import combine_selections
 from genome_sampler.summarize import summarize_selections
-from genome_sampler.label_seqs import label_seqs
+from genome_sampler.label_seqs import label_seqs, label_unaligned_seqs
 from genome_sampler.mask import mask
 
 citations = Citations.load('citations.bib', package='genome_sampler')
@@ -416,7 +416,7 @@ def _5(fmt: VCFLikeMaskFormat) -> pd.DataFrame:
     output_descriptions={
         'labeled_seqs': 'The re-labeled sequences.'
     },
-    name='Re-label sequences',
+    name='Re-label aligned sequences',
     description='Modifies sequence identifiers either by adding or removing'
                 ' metadata. If metadata and one or more columns are provided,'
                 ' the specified metadata columns will be added to the sequence'
@@ -426,6 +426,40 @@ def _5(fmt: VCFLikeMaskFormat) -> pd.DataFrame:
                 ' that will be removed from all sequence ids.'
 )
 
+plugin.methods.register_function(
+    function=label_unaligned_seqs,
+    inputs={'seqs': FeatureData[Sequence]},
+    parameters={
+        'delimiter': Str % Choices('|', ',', '+', ':', ';'),
+        'metadata': Metadata,
+        'columns': List[Str],
+        'missing_value': Str,
+    },
+    outputs=[('labeled_seqs', FeatureData[Sequence])],
+    input_descriptions={'seqs': 'The sequences to be re-labeled.'},
+    parameter_descriptions={
+        'delimiter': 'The delimiter between the sequence id and each metadata'
+                     ' entry.',
+        'metadata': 'The metadata to embed in the header.',
+        'columns': 'The columns in the metadata to be used.',
+        'missing_value': 'Value to use to indicate missing metadata column '
+                         'values for sequences.'
+    },
+    output_descriptions={
+        'labeled_seqs': 'The re-labeled sequences.'
+    },
+    name='Re-label unaligned sequences (deprecated)',
+    description='Modifies sequence identifiers either by adding or removing'
+                ' metadata. If metadata and one or more columns are provided,'
+                ' the specified metadata columns will be added to the sequence'
+                ' id following the original sequence id and separated by'
+                ' `delimiter`. If metadata and columns are not provided, the'
+                ' first occurrence of delimiter and any characters following'
+                ' that will be removed from all sequence ids. DEPRECATED: this'
+                ' will be accessible through `label_seqs`.'
+
+)
+
 
 plugin.visualizers.register_function(
     function=summarize_selections,