Update MEO Node ID Error

spras/meo.py

@@ -10,6 +10,8 @@
 
 __all__ = ['MEO', 'write_properties']
 
+# replaces all underscores in the node names with unicode seperator
+underscore_replacement = '꧁SEP꧂'
 
 # Only supports the Random orientation algorithm
 # Does not support MINSAT or MAXCSP
@@ -88,14 +90,18 @@ 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 underscore_replacement
+            nodes['NODEID'] = nodes['NODEID'].str.replace('_', underscore_replacement)
             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('_', underscore_replacement)
+        edges['Interactor2'] = edges['Interactor2'].str.replace('_', underscore_replacement)
         edges.to_csv(filename_map['edges'], sep='\t', index=False,
                      columns=['Interactor1', 'EdgeType', 'Interactor2', 'Weight'], header=False)
 
@@ -181,6 +187,9 @@ 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 underscore_replacement with _
+            df['Source'] = df['Source'].str.replace(underscore_replacement, '_')
+            df['Target'] = df['Target'].str.replace(underscore_replacement, '_')
             # Keep only edges that were assigned an orientation (direction)
             df = df.loc[df['Oriented']]
             # TODO what should be the edge rank?

test/parse-outputs/expected/meo-pathway-expected.txt

@@ -1,3 +1,3 @@
 Node1	Node2	Rank	Direction
-GENEA	GENEC	1	D
-GENEC	GENEB	1	D
+GENE_A	GENE_C	1	D
+GENE_C	GENEB	1	D

test/parse-outputs/input/meo-raw-pathway.txt

@@ -1,3 +1,3 @@
 Source	Type	Target	Oriented	Weight
-GENEA	pp	GENEC	true	0.5
-GENEC	pd	GENEB	true	0.5
+GENE꧁SEP꧂A	pp	GENE꧁SEP꧂C	true	0.5
+GENE꧁SEP꧂C	pd	GENEB	true	0.5