Added .txt support

MetaSys-LISBP · May 17, 2022 · d4f48d3 · d4f48d3
1 parent 9235bec
commit d4f48d3
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/physiofit/base/io.py b/physiofit/base/io.py
@@ -67,15 +67,15 @@ def _read_data(path_to_data: str) -> DataFrame:
 
         data_path = Path(path_to_data).resolve()
 
-        if data_path.suffix == ".tsv":
+        if data_path.suffix in [".txt", ".tsv"]:
             data = read_csv(str(data_path), sep="\t")
         elif data_path.suffix == ".csv":
             data = read_csv(str(data_path), sep=";")
         else:
             if not data_path.exists():
                 raise ValueError(f"{data_path} is not a valid file")
             else:
-                raise TypeError(f"{data_path} is not a valid format. Accepted formats are .csv or .tsv")
+                raise TypeError(f"{data_path} is not a valid format. Accepted formats are .csv, .txt or .tsv")
 
         IoHandler._verify_data(data)
         return data

diff --git a/physiofit/ui/cli.py b/physiofit/ui/cli.py
@@ -82,7 +82,7 @@ def parse_args():
     parser = argparse.ArgumentParser("Physiofit: Extracellular flux estimation software")
 
     # Parse data arguments (tsv + json)
-    parser.add_argument("-t", "--data", type=str, help="Path to data file in tsv format")
+    parser.add_argument("-t", "--data", type=str, help="Path to data file in tabulated format (txt or tsv)")
     parser.add_argument("-c", "--config", type=str, help="Path to config file in json format")
 
     # Parse basic parameters