Merge pull request #190 from ntalluri/meo_node_id_error

Update MEO Node ID Error

spras/meo.py

@@ -10,6 +10,11 @@
 
 __all__ = ['MEO', 'write_properties']
 
+# replaces all underscores in the node names with unicode seperator
+# MEO keeps only the substring up to the first underscore when parsing node names
+# https://github.com/agitter/meo/blob/1fe57e8ff3952c494e2b14dfdc563a84596e2fcd/src/alg/Vertex.java#L56-L71
+underscore_replacement = '꧁SEP꧂'
+
 
 # Only supports the Random orientation algorithm
 # Does not support MINSAT or MAXCSP
@@ -63,6 +68,8 @@ def write_properties(filename=Path('properties.txt'), edges=None, sources=None,
 - MEO tracks the directionality of the original edges, but all of its output edges are directed.
 - To remain accurate to MEO's design we will also treat the output graph's as directed
 """
+
+
 class MEO(PRM):
     required_inputs = ['sources', 'targets', 'edges']
 
@@ -88,18 +95,21 @@ 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)
 
-
     # TODO add parameter validation
     # TODO document required arguments
     @staticmethod
@@ -181,6 +191,9 @@ 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/generate-inputs/expected/allpairs-network-expected.txt

@@ -1,3 +1,3 @@
 #Interactor1	Interactor2	Weight
-A	B	0.98
+test_A	B	0.98
 B	C	0.77

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

@@ -1,3 +1,3 @@
 ID_interactor_A	ppi	ID_interactor_B
-ENSG0A	ppi	ENSG0B
+ENSG0test_A	ppi	ENSG0B
 ENSG0B	ppi	ENSG0C

test/generate-inputs/expected/meo-edges-expected.txt

@@ -1,2 +1,2 @@
-A	(pp)	B	0.98
+test꧁SEP꧂A	(pp)	B	0.98
 B	(pp)	C	0.77

test/generate-inputs/expected/mincostflow-edges-expected.txt

@@ -1,4 +1,4 @@
-A	B	0.98
+test_A	B	0.98
 B	C	0.77
-B	A	0.98
+B	test_A	0.98
 C	B	0.77

test/generate-inputs/expected/omicsintegrator1-edges-expected.txt

@@ -1,3 +1,3 @@
 protein1	protein2	weight	directionality
-A	B	0.98	U
+test_A	B	0.98	U
 B	C	0.77	U

test/generate-inputs/expected/omicsintegrator2-edges-expected.txt

@@ -1,3 +1,3 @@
 protein1	protein2	cost
-A	B	0.52
+test_A	B	0.52
 B	C	0.73

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

@@ -1,5 +1,5 @@
 #Interactor1	Interactor2	Weight
-A	B	0.98
+test_A	B	0.98
 B	C	0.77
-B	A	0.98
+B	test_A	0.98
 C	B	0.77

test/generate-inputs/inputs/network.txt

@@ -0,0 +1,2 @@
+test_A	B	0.98	U
+B	C	0.77	U

test/generate-inputs/inputs/node-prizes.txt

@@ -0,0 +1,3 @@
+NODEID	prize	active
+test_A	2	true
+C	5.7	true

test/generate-inputs/inputs/sources.txt

@@ -0,0 +1 @@
+test_A

test/generate-inputs/inputs/targets.txt

@@ -0,0 +1 @@
+C

test/generate-inputs/inputs/test_config.yaml

@@ -0,0 +1,69 @@
+hash_length: 7
+container_framework: docker
+unpack_singularity: false
+container_registry:
+   base_url: docker.io
+   owner: reedcompbio
+
+algorithms:
+      - name: "pathlinker"
+        params:
+              include: true
+              run1:
+                  k: range(100,201,100)
+
+      - name: "omicsintegrator1"
+        params:
+              include: true
+              run1:
+                  b: [5, 6]
+                  w: np.linspace(0,5,2)
+                  d: [10]
+
+      - name: "omicsintegrator2"
+        params:
+              include: true
+              run1:
+                  b: [4]
+                  g: [0]
+              run2:
+                  b: [2]
+                  g: [3]
+
+      - name: "meo"
+        params:
+              include: true
+              run1:
+                  max_path_length: [3]
+                  local_search: ["Yes"]
+                  rand_restarts: [10]
+
+      - name: "mincostflow"
+        params:
+              include: true
+              run1:
+                  flow: [1] # The flow must be an int
+                  capacity: [1]
+
+      - name: "allpairs"
+        params:
+              include: true
+
+      - name: "domino"
+        params:
+              include: true
+              run1:
+                  slice_threshold: [0.3]
+                  module_threshold: [0.05]
+
+datasets:
+    -
+      # Labels can only contain letters, numbers, or underscores
+      label: test_data
+      node_files: ["node-prizes.txt", "sources.txt", "targets.txt"]
+      # DataLoader.py can currently only load a single edge file, which is the primary network
+      edge_files: ["network.txt"]
+      # Placeholder
+      other_files: []
+      # Relative path from the spras directory
+      data_dir: "test/generate-inputs/inputs"

test/generate-inputs/test_generate_inputs.py

@@ -17,7 +17,7 @@
     'domino': 'network',
     'pathlinker': 'network',
     'allpairs': 'network'
-    }
+}
 
 
 class TestGenerateInputs:
@@ -29,14 +29,14 @@ def setup_class(cls):
         Path(OUTDIR).mkdir(parents=True, exist_ok=True)
 
     def test_prepare_inputs_networks(self):
-        config_loc = os.path.join("config", "config.yaml")
+        config_loc = os.path.join("test", "generate-inputs", "inputs", "test_config.yaml")
 
         with open(config_loc) as config_file:
             config = yaml.load(config_file, Loader=yaml.FullLoader)
         test_file = "test/generate-inputs/output/test_pickled_dataset.pkl"
 
-        data0_dataset = next((ds for ds in config["datasets"] if ds["label"] == "data0"), None)
-        runner.merge_input(data0_dataset, test_file)
+        test_dataset = next((ds for ds in config["datasets"] if ds["label"] == "test_data"), None)
+        runner.merge_input(test_dataset, test_file)
 
         for algo in algo_exp_file.keys():
             inputs = runner.get_required_inputs(algo)

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