[ENH] Add option to automatically rename table attributes when matching genes with match_table_attributes

orangecontrib/bioinformatics/ncbi/gene/__init__.py

@@ -42,7 +42,7 @@ def load_attributes(self, values: Tuple[str, ...], attributes: Tuple[str, ...] =
             setattr(self, attr, json.loads(val) if attr in ('synonyms', 'db_refs', 'homologs') else val)
 
     def homolog_gene(self, taxonomy_id: str) -> Optional[str]:
-        """ Returns gene homolog for given organism.
+        """Returns gene homolog for given organism.
 
         Parameters
         ----------
@@ -95,7 +95,7 @@ def genes(self, genes: List[str]) -> None:
             self._match()
 
     def get_known_genes(self) -> List[Gene]:
-        """ Return Genes with known Entrez ID
+        """Return Genes with known Entrez ID
 
         Returns
         -------
@@ -106,7 +106,7 @@ def get_known_genes(self) -> List[Gene]:
         return [gene for gene in self.genes if gene.gene_id]
 
     def to_data_table(self, selected_genes: Optional[List[str]] = None) -> Table:
-        """ Transform GeneMatcher results to Orange data table.
+        """Transform GeneMatcher results to Orange data table.
 
         Optionally we can provide a list of genes (Entrez Ids).
         The table on the output will be populated only with provided genes.
@@ -184,7 +184,7 @@ def to_data_table(self, selected_genes: Optional[List[str]] = None) -> Table:
     def match_table_column(
         self, data_table: Table, column_name: str, target_column: Optional[StringVariable] = None
     ) -> Table:
-        """ Helper function for gene name matching with :class:`Orange.data.Table`.
+        """Helper function for gene name matching with :class:`Orange.data.Table`.
 
         Give a column of genes, GeneMatcher will try to map genes to their
         corresponding Entrez Ids.
@@ -223,8 +223,8 @@ def match_table_column(
 
             return new_data
 
-    def match_table_attributes(self, data_table):
-        """ Helper function for gene name matching with :class:`Orange.data.Table`.
+    def match_table_attributes(self, data_table, rename=False, source_name='Source ID') -> Table:
+        """Helper function for gene name matching with :class:`Orange.data.Table`.
 
         Match table attributes and if a unique match is found create a new column attribute
         for Entrez Id. Attribute name is defined here: `orangecontrib.bioinformatics.ncbi.gene.config.NCBI_ID`
@@ -237,18 +237,28 @@ def match_table_attributes(self, data_table):
 
         Returns
         -------
+
         :class:`Orange.data.Table`
             Data table column attributes are populated with Entrez Ids
 
         """
-        input_gene_names = [var.name for var in data_table.domain.attributes]
 
-        if input_gene_names:
-            self.genes = input_gene_names
+        # run gene matcher
+        self.genes = [var.name for var in data_table.domain.attributes]
+
+        def helper(gene, attribute):
+            if gene.gene_id:
+                if rename:
+                    attribute = attribute.renamed(gene.symbol)
+                    attribute.attributes[source_name] = gene.input_identifier
+
+                attribute.attributes[ENTREZ_ID] = gene.gene_id
+            return attribute
+
+        attributes = [helper(gene, attr) for gene, attr in zip(self.genes, data_table.domain.attributes)]
+        domain = Domain(attributes, data_table.domain.class_vars, data_table.domain.metas)
 
-            for gene in self.genes:
-                if gene.gene_id:
-                    data_table.domain[gene.input_identifier].attributes[ENTREZ_ID] = gene.gene_id
+        return data_table.transform(domain)
 
     def match_genes(self):
         self._match()
@@ -299,7 +309,7 @@ def _match(self):
 
 class GeneInfo(dict):
     def __init__(self, tax_id: str):
-        """ Loads genes for given organism in a dict.
+        """Loads genes for given organism in a dict.
 
         Each instance of :class:`Gene` is mapped to corresponding Entrez ID
 

orangecontrib/bioinformatics/tests/ncbi/test_gene.py

@@ -81,10 +81,11 @@ def test_match_table_attributes(self):
 
         data = Table('brown-selected.tab')
         data = Table.transpose(data, feature_names_column='gene')
-        gm.match_table_attributes(data)
+        data = gm.match_table_attributes(data, rename=True, source_name='FooBar')
 
         for column in data.domain.attributes:
             self.assertTrue(ENTREZ_ID in column.attributes)
+            self.assertTrue('FooBar' in column.attributes)
 
 
 class TestGeneInfo(unittest.TestCase):

orangecontrib/bioinformatics/widgets/OWGenialisExpressions.py

@@ -668,7 +668,7 @@ def set_progress():
     state.set_status('Matching genes ...')
     tax_id = species_name_to_taxid(species)
     gm = GeneMatcher(tax_id)
-    gm.match_table_attributes(table)
+    table = gm.match_table_attributes(table, rename=True)
     table.attributes[TableAnnotation.tax_id] = tax_id
     table.attributes[TableAnnotation.gene_as_attr_name] = True
     table.attributes[TableAnnotation.gene_id_attribute] = 'Entrez ID'

orangecontrib/bioinformatics/widgets/OWdictyExpress.py

@@ -260,7 +260,7 @@ def send_to_output(self, result):
                 data = gene_matcher.match_table_column(data, 'Gene', StringVariable(ENTREZ_ID))
             data.attributes[GENE_ID_COLUMN] = ENTREZ_ID
         else:
-            gene_matcher.match_table_attributes(data)
+            data = gene_matcher.match_table_attributes(data)
             data.attributes[GENE_ID_ATTRIBUTE] = ENTREZ_ID
 
         # add table attributes