added header to var output

GrAnnoT/Functions_output.py

@@ -128,7 +128,7 @@ def transfer_on_target(segments_file, out_gff, out_var,out_aln,target_genome,tar
 
         if not args.annotation:
             # cov and id filter tests (if not done in annotation) 
-            for feature_id in tqdm(list_feature_to_transfer,desc="        Computing the coverage and sequence id of the features before transfer",disable=not args.verbose):
+            for feature_id in tqdm(list_feature_to_transfer,desc="        Computing the coverage and sequence id of the features before transfer",unit=' feature',disable=not args.verbose):
                 feature=Features[feature_id]
                 if feature.parent=="": # usually a gene
                     for match in feature.segments_list_target:
@@ -144,6 +144,7 @@ def transfer_on_target(segments_file, out_gff, out_var,out_aln,target_genome,tar
     if args.variation:
         seg_seq=get_segments_sequence(segments_file,segments_list)
         with open(out_var, 'w') as file_out_var:
+            file_out_var.write(f'# feature_id\tfeature_type\tsequence_id\ttarget_start_position\ttarget_stop_position\ttarget_feature_length\tinversion\tlength_difference\tvariation_type\tref_sequence\talt_sequence\tvariation_length\tvariation_position_on_source_feature\tvariation_position_on_target_feature\n')
 
             for feat in tqdm(list_feature_to_transfer,desc=f'        Generating {target_genome} genes variation details',unit=" feature",disable=not args.verbose):
                 feature=Features[feat]
@@ -428,7 +429,7 @@ def detect_small_inversion(variation):
 # print a deletion at the end of a feature
 def print_last_deletion(variation,feature_path_source_genome,i,feat_start,feature,seg_seq):
     seg_del=search_segment(feature_path_source_genome[i])
-    pos_old=int(Segments[seg_del].start)-int(feat_start)+1
+    pos_old=int(Segments[seg_del].get_start(feature.id))-int(feat_start)+1
 
     del_sequence=get_sequence_list_seg(feature_path_source_genome,i,feature,seg_seq)
     length=len(del_sequence)