added flag for solo ltrs

nested/cli/nester.py

@@ -27,8 +27,9 @@ from nested.utils.dependency_resolver import DependencyResolver
 @click.option('--discovery_tool', '-dt', default=DiscoveryTool.LTR_finder.name,
     type=click.Choice(list(map(lambda val: val, DiscoveryTool.__members__))),
     help='Determines which tool is used for retrotransoson discovery. Default: LTR_finder')
+@click.option('--solo_ltrs', '-solo', is_flag=True, default=False, help='Run solo LTR module')
 def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initial_threshold, 
-        threshold_multiplier, threads, discovery_tool):
+        threshold_multiplier, threads, discovery_tool, solo_ltrs):
     check_ram(input_fasta, threads)
     check_permissions(output_folder, os.W_OK | os.X_OK)
     number_of_errors = [0]
@@ -41,21 +42,24 @@ def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initia
             futuress.append(executor.submit(process_sequence, sequence, sketcher, 
                 sketch, format, output_fasta_offset, output_folder, 
                 initial_threshold, threshold_multiplier, number_of_errors,
-                dependencyResolver))
+                dependencyResolver, solo_ltrs))
         futures.wait(futuress)
     end_time = datetime.now()
     print('Total time: {}'.format(end_time - start_time))
     print('Number of errors: {}'.format(number_of_errors[0]))
 
-def process_sequence(sequence, sketcher, sketch, format, output_fasta_offset, output_folder, initial_threshold, threshold_multiplier, errors, dependency_resolver):
+def process_sequence(sequence, sketcher, sketch, format, output_fasta_offset, output_folder, initial_threshold, threshold_multiplier, errors, dependency_resolver, solo_ltrs):
     sequence.id = sequence.id.replace('/', '--')
     seq_start_time = datetime.now()
     strlen = 15
     print("Processing {}".format(sequence.id))
     try:
-        nester = Nester(sequence, initial_threshold, threshold_multiplier, dependency_resolver)
+        nester = Nester(sequence, initial_threshold, threshold_multiplier, dependency_resolver, solo_ltrs)
         sketcher.create_gff(nester.nested_element, dirpath=output_folder, output_fasta_offset=output_fasta_offset, format=format)
-        sketcher.create_solo_ltr_gff(nester.solo_ltrs, dirpath=output_folder)
+        
+        if solo_ltrs:
+            sketcher.create_solo_ltr_gff(nester.solo_ltrs, dirpath=output_folder)
+            
         sketcher.create_trf_gff(nester.trf, nester.seqid, dirpath=output_folder)
         if sketch:
             if format != 'default':

nested/core/nester.py

@@ -21,7 +21,7 @@ class Nester(ToolInterface):
         nested_element (NestedElement): nested element
     """
 
-    def __init__(self, sequence, threshold, multiplier, dependency_resolver):
+    def __init__(self, sequence, threshold, multiplier, dependency_resolver, solo):
         self.seqid = sequence.id
         self.sequence = sequence.seq
         self.nested_element = None
@@ -32,6 +32,7 @@ class Nester(ToolInterface):
         self.multiplier = multiplier
         self.dependency_resolver = dependency_resolver
         self.trf = []
+        self.solo = solo
         self._find_nesting()
 
     def _find_nesting(self):
@@ -56,9 +57,11 @@ class Nester(ToolInterface):
         if not candidates:
             best_candidate = gene.get_best_candidate()
             if not best_candidate:
-                self.solo_ltrs.find_solo_ltrs(sequence)
-                self.solo_ltrs.solo_ltrs.sort(key=lambda x: x.location[0], reverse=True)
-                return self.solo_ltrs.solo_ltrs
+                if solo:
+                    self.solo_ltrs.find_solo_ltrs(sequence)
+                    self.solo_ltrs.solo_ltrs.sort(key=lambda x: x.location[0], reverse=True)
+                    return self.solo_ltrs.solo_ltrs
+                return []
             candidates = [best_candidate]
 
         # sort by score (from highest)