fix: correct reading multiple lines for amrfinder

NBChub · Jul 15, 2024 · f796d1c · f796d1c
1 parent 4d8cd79
commit f796d1c
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/.examples/Lactobacillus_delbrueckii/project_config.yaml b/.examples/Lactobacillus_delbrueckii/project_config.yaml
@@ -29,4 +29,4 @@ rules:
   cblaster-genome: TRUE
   cblaster-bgc: FALSE
   gecco: TRUE
-  amrfinderplus: TRUE
+  amrfinderplus: FALSE
diff --git a/workflow/bgcflow/bgcflow/data/gather_amrfinder.py b/workflow/bgcflow/bgcflow/data/gather_amrfinder.py
@@ -53,9 +53,9 @@ def gather_amrfinder(input_list, output_file):
     dataframes = []
 
     with open(input_list, "r") as f:
-        data = f.readlines()
+        data = f.read()
 
-    dataframes = pd.concat([cleanup_amrfinder(i.strip("\n")) for i in data])
+    dataframes = pd.concat([cleanup_amrfinder(i) for i in data.split()])
     dataframes.to_csv(output_file, index=False)
     return