fixed error oi2 error

ntalluri · Sep 3, 2024 · ea88614 · ea88614
1 parent b202639
commit ea88614
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/spras/omicsintegrator2.py b/spras/omicsintegrator2.py
@@ -148,9 +148,7 @@ def parse_output(raw_pathway_file, standardized_pathway_file):
         """
         # Omicsintegrator2 returns a single line file if no network is found
         num_lines = sum(1 for line in open(raw_pathway_file))
-        df = pd.read_csv(raw_pathway_file, sep='\t', header=0)
-        print(df)
-        # Omicsintegrator2 has corrupted output, list of correct column names and order
+        # Omicsintegrator2 has corrupted output; list of correct column names and order
         correct_columns = ['protein1', 'protein2', 'cost', 'in_solution']
 
         if num_lines < 2:

diff --git a/test/parse-outputs/test_parse_outputs.py b/test/parse-outputs/test_parse_outputs.py
@@ -14,6 +14,7 @@
 
 algorithms = ['mincostflow', 'meo', 'omicsintegrator1', 'omicsintegrator2', 'pathlinker', 'allpairs', 'domino']
 
+
 class TestParseOutputs:
     @classmethod
     def setup_class(cls):
@@ -38,14 +39,14 @@ def test_empty_file(self):
             runner.parse_output(algo, test_file, out_file)
             assert filecmp.cmp(OUTDIR + f"{algo}-empty-pathway.txt", EXPDIR + f"empty-pathway-expected.txt", shallow=False)
 
-    def test_oi2_miss_insolution_parse_output(self):
+    def test_oi2_miss_insolution(self):
         test_file = RAW_PATHS_INDIR + f"oi2-miss-insolution.txt"
         out_file = OUTDIR + f"oi2-miss-insolution-pathway.txt"
 
         runner.parse_output('omicsintegrator2', test_file, out_file)
         assert filecmp.cmp(out_file, EXPDIR + f"empty-pathway-expected.txt", shallow=False)
 
-    def test_oi2_wrong_order_parse_output(self):
+    def test_oi2_wrong_order(self):
         test_file = RAW_PATHS_INDIR + f"oi2-wrong-order.txt"
         out_file = OUTDIR + f"oi2-wrong-order-pathway.txt"