feat(rpfbagr): allow medium file fmt csv and tsv

src/rpfbagr/__main__.py

@@ -82,7 +82,7 @@ def main():
     parser_medium.add_argument(
         "--input-medium-file",
         type=str,
-        help="Provide a csv file with an header as <coumpond_id>,"
+        help="Provide a csv or tsv file with an header as <coumpond_id>,"
         "<lower_bound>, <upper_bound>. This file "
         "provides information about metabolites (Metanetx Id) "
         "to add or remove.",

src/rpfbagr/medium.py

@@ -1,3 +1,4 @@
+import csv
 import logging
 from collections import OrderedDict
 
@@ -6,8 +7,16 @@
 
 
 def load_medium(path: str) -> dict:
+    # Find delimiter.
+    with open(path) as fid:
+        dialect = csv.Sniffer().sniff(fid.readline())
+    # Load.
     df = pd.read_csv(
-        path, header=None, index_col=0, names=["reaction", "lower", "upper"]
+        path,
+        header=None,
+        index_col=0,
+        names=["reaction", "lower", "upper"],
+        sep=dialect.delimiter,
     )
     medium = df.to_dict("index")
     envcond = OrderedDict()

tests/dataset/medium/butanol.tsv

@@ -0,0 +1,2 @@
+EX_glc__D_e	-10.0	10.0
+EX_o2_e	-5.0	5.0

tests/main_test.py

@@ -6,7 +6,8 @@ class Main_test(unittest.TestCase):
     dataset_path = os.path.join(os.path.dirname(__file__), "dataset")
     # Medium.
     medium_path = os.path.join(dataset_path, "medium")
-    medium_butanol = os.path.join(medium_path, "butanol.csv")
+    medium_butanol_csv = os.path.join(medium_path, "butanol.csv")
+    medium_butanol_tsv = os.path.join(medium_path, "butanol.tsv")
     # Model.
     model_path = os.path.join(dataset_path, "model")
     model_ecoli = os.path.join(model_path, "iAF1260.xml")

tests/test_medium.py

@@ -8,14 +8,14 @@
 
 class Test_functional(Main_test):
     def test_load_medium(self):
-        medium = load_medium(self.medium_butanol)
+        medium = load_medium(self.medium_butanol_csv)
         theorical_medium = OrderedDict(
             {"EX_glc__D_e": (-10.0, 10.0), "EX_o2_e": (-5.0, 5.0)}
         )
         self.assertEqual(medium, theorical_medium)
 
     def test_associate_flux_env(self):
-        medium = load_medium(self.medium_butanol)
+        medium = load_medium(self.medium_butanol_csv)
         model = load_model(self.model_ecoli)
         self.assertEqual(
             model.reactions.get_by_id("EX_glc__D_e").bounds, (-8.0, 999999.0)
@@ -27,3 +27,8 @@ def test_associate_flux_env(self):
         )
         self.assertEqual(model.reactions.get_by_id("EX_glc__D_e").bounds, (-10.0, 10.0))
         self.assertEqual(model.reactions.get_by_id("EX_o2_e").bounds, (-5.0, 5.0))
+
+    def test_format(self):
+        medium_csv = load_medium(self.medium_butanol_csv)
+        medium_tsv = load_medium(self.medium_butanol_tsv)
+        self.assertEqual(medium_csv, medium_tsv)

tests/test_software.py

@@ -29,7 +29,7 @@ def test_software_butanol(self):
             args += ["--output-file-csv", fd.name]
             args += ["--strategy", "ko"]
             args += ["--max-knockouts", "3"]
-            args += ["--input-medium-file", self.medium_butanol]
+            args += ["--input-medium-file", self.medium_butanol_csv]
             args += ["--thread", "1"]
 
             ret = Test_software.launch(args)
@@ -56,7 +56,7 @@ def test_software_butanol_light(self):
             args += ["--output-file-csv", fd.name]
             args += ["--strategy", "ko"]
             args += ["--max-knockouts", "3"]
-            args += ["--input-medium-file", self.medium_butanol]
+            args += ["--input-medium-file", self.medium_butanol_tsv]
             args += ["--thread", "1"]
 
             ret = Test_software.launch(args)
@@ -88,7 +88,7 @@ def test_software_butanol_iml1515(self):
             args += ["--output-file-tsv", fd.name]
             args += ["--strategy", "ko"]
             args += ["--max-knockouts", "3"]
-            args += ["--input-medium-file", self.medium_butanol]
+            args += ["--input-medium-file", self.medium_butanol_csv]
             args += ["--thread", "1"]
 
             ret = Test_software.launch(args)