EI-CoreBioinformatics#240, EI-CoreBioinformatics#243: solved the bug …

…that caused boolean values to be converted into integers.

Mikado/daijin/__init__.py

@@ -372,6 +372,7 @@ def assemble_transcripts_pipeline(args):
                                             prefix="assemble")
     yaml.dump(doc, yaml_file)
     yaml_file.flush()
+    shutil.copystat(args.config, yaml_file.name)
 
     if args.latency_wait is not None:
         latency = abs(args.latency_wait)
@@ -400,7 +401,8 @@ def assemble_transcripts_pipeline(args):
         "printdag": args.dag,
         "forceall": args.dag,
         "forcerun": args.forcerun,
-        "lock": (not args.nolock)
+        "lock": (not args.nolock),
+        "printreason": True
     }
 
     if "configfile" in inspect.getfullargspec(snakemake.snakemake).args:
@@ -494,6 +496,7 @@ def mikado_pipeline(args):
                                             )
     yaml.dump(doc, yaml_file)
     yaml_file.flush()
+    shutil.copystat(args.config, yaml_file.name)
 
     if SCHEDULER == "local":
         hpc_conf = None
@@ -541,6 +544,7 @@ def mikado_pipeline(args):
         "forceall": args.dag,
         "forcerun": args.forcerun,
         "lock": (not args.nolock),
+        "printreason": True
     }
 
     if "configfile" in inspect.getfullargspec(snakemake.snakemake).args:

Mikado/loci/superlocus.py

@@ -935,6 +935,7 @@ def define_subloci(self):
 
         if self.subloci_defined is True:
             return
+
         self.compile_requirements()
         self.subloci = []
 

Mikado/transcripts/transcript.py

@@ -519,6 +519,8 @@ def __initialize_with_gf(self, transcript_row: (GffLine, GtfLine)):
                 pass
             elif val in booleans:
                 val = booleans[val]
+            elif isinstance(val, bool):
+                pass
             else:
                 try:
                     val = int(val)
@@ -994,7 +996,7 @@ def is_reference(self, value):
                 value = False
             else:
                 pass
-        if value not in (False, True, None):
+        if not isinstance(value, bool) and value is not None:
             raise ValueError("Invalid value: {} (type: {})".format(value, type(value)))
         self.__is_reference = value
 
@@ -2824,7 +2826,7 @@ def has_start_codon(self):
     def has_start_codon(self, value):
         """Setter. Checks that the argument is boolean."""
 
-        if value not in (None, False, True):
+        if not isinstance(value, bool) and value is not None:
             raise TypeError(
                 "Invalid value for has_start_codon: {0}".format(type(value)))
         self.__has_start_codon = value
@@ -2841,7 +2843,7 @@ def has_stop_codon(self):
     def has_stop_codon(self, value):
         """Setter. Checks that the argument is boolean."""
 
-        if value not in (None, False, True):
+        if not isinstance(value, bool) and value is not None:
             raise TypeError(
                 "Invalid value for has_stop_codon: {0}".format(type(value)))
 
@@ -3539,7 +3541,7 @@ def suspicious_splicing(self):
 
         mixed = bool(self.attributes.get("mixed_splices", False))
         canonical_on_reverse = self.attributes.get("canonical_on_reverse_strand", False)
-        if canonical_on_reverse not in (True, False):
+        if not isinstance(canonical_on_reverse, bool):
             canonical_on_reverse = literal_eval(canonical_on_reverse)
             self.attributes["canonical_on_reverse_strand"] = canonical_on_reverse