Merge pull request #426 from Reed-CompBio/rwr-direction

fix(rwr,strwr): directionality conversions

Author: tristan-f-r

spras/rwr.py

@@ -4,7 +4,10 @@
 
 from spras.containers import prepare_volume, run_container_and_log
 from spras.dataset import Dataset
-from spras.interactome import reinsert_direction_col_directed
+from spras.interactome import (
+    convert_undirected_to_directed,
+    reinsert_direction_col_directed,
+)
 from spras.prm import PRM
 from spras.util import add_rank_column, duplicate_edges, raw_pathway_df
 
@@ -29,6 +32,8 @@ def generate_inputs(data, filename_map):
 
         # Get edge data for network file
         edges = data.get_interactome()
+        edges = convert_undirected_to_directed(edges)
+
         edges.to_csv(filename_map['network'],sep='|',index=False,columns=['Interactor1','Interactor2'],header=False)
 
     @staticmethod

spras/strwr.py

@@ -2,7 +2,10 @@
 
 from spras.containers import prepare_volume, run_container_and_log
 from spras.dataset import Dataset
-from spras.interactome import reinsert_direction_col_directed
+from spras.interactome import (
+    convert_undirected_to_directed,
+    reinsert_direction_col_directed,
+)
 from spras.prm import PRM
 from spras.util import add_rank_column, duplicate_edges, raw_pathway_df
 
@@ -29,6 +32,8 @@ def generate_inputs(data, filename_map):
 
         # Get edge data for network file
         edges = data.get_interactome()
+        edges = convert_undirected_to_directed(edges)
+
         edges.to_csv(filename_map['network'],sep='|',index=False,columns=['Interactor1','Interactor2'],header=False)
 
     @staticmethod

test/generate-inputs/expected/rwr-network-expected.txt

@@ -1,2 +1,4 @@
 test_A|B
 B|C
+B|test_A
+C|B

test/generate-inputs/expected/strwr-network-expected.txt

@@ -1,2 +1,4 @@
 test_A|B
 B|C
+B|test_A
+C|B