[FIX](seqpos): replace seqpos

biobb_dna/backbone/bipopulations.py

@@ -95,10 +95,12 @@ def __init__(
 
         self.properties = properties
         self.sequence = properties.get("sequence")
+        # self.seqpos = properties.get("seqpos", None)
         self.seqpos = [
-            int(item) for item in _from_string_to_list(properties.get("seqpos", None))
+            int(elem) for elem in _from_string_to_list(properties.get("seqpos", None))
         ]
-
+        print("seqpos::::::::")
+        print(self.seqpos)
         # Check the properties
         self.check_properties(properties)
         self.check_arguments()
@@ -124,6 +126,8 @@ def launch(self) -> int:
                 )
             if not (isinstance(self.seqpos, list) and len(self.seqpos) > 1):
                 raise ValueError("seqpos must be a list of at least two integers")
+        else:
+            self.seqpos = None  # type: ignore
 
         # read input files
         epsilC = read_series(
@@ -192,7 +196,7 @@ def get_xlabels(self, strand1, strand2):
         labelsC[-1] = f"{labelsC[-1]}3'"
         labelsC = [f"{i}-{j}" for i, j in zip(labelsC, range(len(labelsC), 0, -1))]
 
-        if self.seqpos:
+        if self.seqpos is not None:
             labelsC = [labelsC[i] for i in self.seqpos]
             labelsW = [labelsW[i] for i in self.seqpos]
         xlabels = labelsW + ["-"] + labelsC

biobb_dna/backbone/canonicalag.py

@@ -126,6 +126,8 @@ def launch(self) -> int:
                 )
             if not (isinstance(self.seqpos, list) and len(self.seqpos) > 1):
                 raise ValueError("seqpos must be a list of at least two integers")
+        else:
+            self.seqpos = None  # type: ignore
 
         # read input files
         alphaC = read_series(

biobb_dna/backbone/puckering.py

@@ -118,6 +118,8 @@ def launch(self) -> int:
                 )
             if not (isinstance(self.seqpos, list) and len(self.seqpos) > 1):
                 raise ValueError("seqpos must be a list of at least two integers")
+        else:
+            self.seqpos = None  # type: ignore
 
         # read input files
         phaseC = read_series(

biobb_dna/dna/dna_averages.py

@@ -148,6 +148,8 @@ def launch(self) -> int:
                 )
             if not (isinstance(self.seqpos, list) and len(self.seqpos) > 1):
                 raise ValueError("seqpos must be a list of at least two integers")
+        else:
+            self.seqpos = None  # type: ignore
 
         # read input .ser file
         ser_data = read_series(

biobb_dna/stiffness/average_stiffness.py

@@ -146,6 +146,8 @@ def launch(self) -> int:
                 )
             if not (isinstance(self.seqpos, list) and len(self.seqpos) > 1):
                 raise ValueError("seqpos must be a list of at least two integers")
+        else:
+            self.seqpos = None  # type: ignore
 
         # read input .ser file
         ser_data = read_series(

biobb_dna/test/unitests/test_backbone/test_bipopulations.py

@@ -1,21 +1,25 @@
 # type: ignore
+import platform
+
 from biobb_common.tools import test_fixtures as fx
+
 from biobb_dna.backbone.bipopulations import bipopulations
-import platform
 
 
-class TestBIPopulations():
+class TestBIPopulations:
     def setup_class(self):
-        fx.test_setup(self, 'bipopulations')
+        fx.test_setup(self, "bipopulations")
 
     def teardown_class(self):
-        fx.test_teardown(self)
+        pass
+
+    # fx.test_teardown(self)
 
     def test_bipopulations(self):
         returncode = bipopulations(properties=self.properties, **self.paths)
-        assert fx.not_empty(self.paths['output_csv_path'])
-        assert fx.not_empty(self.paths['output_jpg_path'])
+        assert fx.not_empty(self.paths["output_csv_path"])
+        assert fx.not_empty(self.paths["output_jpg_path"])
         assert fx.exe_success(returncode)
-        if platform.system() == 'Darwin':
-            assert fx.equal(self.paths['output_csv_path'], self.paths['ref_csv_output'])
-        assert fx.equal(self.paths['output_jpg_path'], self.paths['ref_jpg_output'])
+        if platform.system() == "Darwin":
+            assert fx.equal(self.paths["output_csv_path"], self.paths["ref_csv_output"])
+        assert fx.equal(self.paths["output_jpg_path"], self.paths["ref_jpg_output"])