update gene selection to include me-type (#146)

bluepyemodel/icselector/icselector.py

@@ -123,29 +123,29 @@ def __set_parameters_from_gene(self, gene_name):
         else:
             logging.warning("Could not determine mechanism for gene %s", gene_name)
 
-    def _set_parameters_from_ttype(self):
+    def _set_parameters_from_mettype(self):
         """Copy parameters from selected genes to mechanims."""
 
         for gene_name in self._gene_selector.selected_genes:
             self.__set_parameters_from_gene(gene_name)
 
-    def _select_genes_from_ttype(self, key_words):
+    def _select_genes_from_mettype(self, mettype):
         """Select genes from key words.
         Args:
-            key_words (list [str]): list of keys to select genes
+            mettype (dict): dict containing the etype, mtype and ttype
         """
 
         # === Get genes from gene mapping file
         logging.info("\n===============\nGenes Selection\n===============")
-        genes = self._gene_selector.select_from_ttype(key_words)
+        genes = self._gene_selector.select_from_mettype(mettype)
         logging.info(str(self._gene_selector))
 
         # === Map genes to channels
         for gene, info in genes.items():
             if gene in self._gene_to_ic:
                 info["channel"] = self._gene_to_ic[gene]
 
-    def _select_mechanisms_from_ttype(self):
+    def _select_mechanisms_from_mettype(self):
         """Select mechanisms from previously selected genes."""
 
         logging.info("\n==================\nChannels Selection\n==================")
@@ -259,12 +259,12 @@ def _get_cell_config(self):
         logging.info(str(config))
         return config
 
-    def get_cell_config_from_ttype(self, key_words):
+    def get_cell_config_from_mettype(self, mettype):
         """Get all information related to cell model configuration from
         mechanisms selected based on genetic expression profiles.
 
         Args:
-            key_words: keys to select MET-types
+            mettype (dict): Dictionary containing the MET-types
 
         Returns:
             parameters (list [dict,]): mechanism parameters per compartment
@@ -274,9 +274,9 @@ def get_cell_config_from_ttype(self, key_words):
         """
 
         # Perform selections
-        self._select_genes_from_ttype(key_words)
-        self._set_parameters_from_ttype()
-        self._select_mechanisms_from_ttype()
+        self._select_genes_from_mettype(mettype)
+        self._set_parameters_from_mettype()
+        self._select_mechanisms_from_mettype()
 
         # Get configuration
         mechs = self._model_selector.get_mechanisms()

bluepyemodel/icselector/modules/gene_selector.py

@@ -183,12 +183,12 @@ def get(self, gene_name):
             return self.selected_genes[gene_name]
         raise KeyError("Gene not available for the selected ttype.")
 
-    def select_from_ttype(self, keys=None, group_compartments=False):
+    def select_from_mettype(self, mettype, group_compartments=False):
         """Returns selected genes and distributions associated with provided
-        key words.
+        mettype.
 
         Args:
-            keys (list [str]): List of keywords
+            mettype (dict): Dictionary containing the etype, mtype and ttype
             group_compartments: Option to combine compartments into groups
             (e.g. 'all', or 'alldend')
 
@@ -197,19 +197,23 @@ def select_from_ttype(self, keys=None, group_compartments=False):
         """
 
         df = self._gene_map
-        if isinstance(keys, str):
-            keys = [keys]
-        if keys:
-            df = self._filter(df, keys)
+
+        me_type = f"{mettype['mtype']}_{mettype['etype']}"
+        t_type = mettype["ttype"]
+
+        # replace double underscores with spaces
+        t_type = t_type.replace("__", " ")
+
+        try:
+            genes = df.loc[(me_type, t_type)]
+        except KeyError as exc:
+            raise ValueError(
+                f"No records found for me-type: {me_type} \
+                             and t-type: {t_type}"
+            ) from exc
+
         # Store result
-        self.selected_met_types = np.unique([f"{v[0]} - {v[1]}" for v in df.index.values])
-        df = df.droplevel([0, 1])
-        # Apply filter also to genes
-        if keys:
-            genes = self._filter(df.T, keys)
-            genes = genes.T
-        else:
-            genes = df
+        self.selected_met_types = [f"{me_type} - {t_type}"]
 
         names = genes.columns.values
         for name in names:

bluepyemodel/model/model_configurator.py

@@ -101,8 +101,13 @@ def get_gene_based_parameters(self):
         ic_map_path = self.access_point.load_ic_map()
 
         selector = icselector.ICSelector(ic_map_path, gene_map_path)
-        parameters, mechanisms, distributions, nexus_keys = selector.get_cell_config_from_ttype(
-            self.access_point.emodel_metadata.ttype
+        mettype = {
+            "etype": self.access_point.emodel_metadata.etype,
+            "mtype": self.access_point.emodel_metadata.mtype,
+            "ttype": self.access_point.emodel_metadata.ttype,
+        }
+        parameters, mechanisms, distributions, nexus_keys = selector.get_cell_config_from_mettype(
+            mettype
         )
 
         return parameters, mechanisms, distributions, nexus_keys