update code to pre and post process underscores in node names

spras/meo.py

@@ -88,14 +88,18 @@ def generate_inputs(data, filename_map):
             # TODO test whether this selection is needed, what values could the column contain that we would want to
             # include or exclude?
             nodes = nodes.loc[nodes[node_type]]
+            # replace _'s with ꧁SEP꧂
+            nodes['NODEID'] = nodes['NODEID'].str.replace('_', '꧁SEP꧂')
             nodes.to_csv(filename_map[node_type], index=False, columns=['NODEID'], header=False)
 
         # Create network file
         edges = data.get_interactome()
 
         # Format network file
         edges = add_directionality_constant(edges, 'EdgeType', '(pd)', '(pp)')
-
+        # replace _'s with ꧁SEP꧂
+        edges['Interactor1'] = edges['Interactor1'].str.replace('_', '꧁SEP꧂')
+        edges['Interactor2'] = edges['Interactor2'].str.replace('_', '꧁SEP꧂')
         edges.to_csv(filename_map['edges'], sep='\t', index=False,
                      columns=['Interactor1', 'EdgeType', 'Interactor2', 'Weight'], header=False)
 
@@ -181,6 +185,9 @@ def parse_output(raw_pathway_file, standardized_pathway_file):
         # Columns Source Type Target Oriented Weight
         df = raw_pathway_df(raw_pathway_file, sep='\t', header=0)
         if not df.empty:
+            # Replace ꧁SEP꧂ with _
+            df['Source'] = df['Source'].str.replace('꧁SEP꧂', '_')
+            df['Target'] = df['Target'].str.replace('꧁SEP꧂', '_')
             # Keep only edges that were assigned an orientation (direction)
             df = df.loc[df['Oriented']]
             # TODO what should be the edge rank?

test/MEO/input/meo-edges.txt

@@ -1,6 +1,6 @@
-GeneA	(pp)	GeneC	0.5
-GeneB	(pp)	GeneC	0.5
-GeneC	(pp)	GeneD	0.5
+Gene_A	(pp)	Gene_C	0.5
+GeneB	(pp)	Gene_C	0.5
+Gene_C	(pp)	GeneD	0.5
 GeneD	(pp)	GeneE	0.5
 GeneD	(pp)	GeneG	0.5
 GeneE	(pp)	GeneF	0.5