add updated scripts

nested/core/executor.py

@@ -22,9 +22,9 @@ class Executor:
             new_elements = module.tool.run(self.sequence.seq)
             self._crop_sequence(new_elements)
             elements += new_elements
-
+        
         self._recalculate_coordinates(elements)
-
+        
         for module in self.modules:
             if hasattr(module.output_generator, "__iter__"):
                 for generator in module.output_generator:

nested/core/tools/retro_te_domains.py

@@ -37,7 +37,7 @@ class RetroTeDomains(ToolInterface):
         
         retro_domains = self._filter_candidates(candidates)
 
-        retro_domains.sort(key=lambda e: e.location[0])
+        retro_domains.sort(key=lambda e: e.location[0], reverse=True)
         self.output_object = RetroDomainOutputObject(self.seqId, sequence, retro_domains)
         return retro_domains
 
@@ -45,8 +45,12 @@ class RetroTeDomains(ToolInterface):
         retro_domains = []
         # filter on matches with evalue 0.1 and lower
         candidates = [candidate for candidate in candidates if candidate.evalue <= 0.1]
+        
+        for c in candidates:
+            c.location.sort()
+        
         # sort after location and score
-        candidates.sort(key=lambda e: (e.location, -e.score))
+        candidates.sort(key=lambda e: (e.location[0], -e.score))
         for candidate in candidates:
             add = True
             for domain in retro_domains:

nested/output/output_generators/retro_domain_output_generator.py

@@ -12,6 +12,11 @@ class RetroDomainOutputGenerator(BaseOutputGenerator):
     def generate_output(self, output_object: RetroDomainOutputObject) -> NoReturn:
         self.create_data_directory(output_object.sequence_id)
         
+        # sort elements after location[0]
+        for element in output_object.elements:
+            element.location = [min(element.location), max(element.location)]
+        output_object.elements.sort(key=lambda e: e.location[0])
+
         with open(f"{self.directory}/{output_object.sequence_id}/{output_object.sequence_id}_retro_domain.gff", "w+") as gff:
             i = 0
             gff.write("##gff-version 3\n")
@@ -20,7 +25,6 @@ class RetroDomainOutputGenerator(BaseOutputGenerator):
                 sign = (lambda x: x and (1, -1)[x < 0])(domain.frame[0])
                 strand = "+"
                 if sign < 0:
-                    domain_location = [domain_location[1], domain_location[0]]
                     strand = '-'                
                 gff.write(output_object.sequence_id + "\t"
                           + "retroTeDomain\tpolypeptide_conserved_region\t"