modifié l'output pour les substitutions de n bases pour m bases.

Functions_output.py

@@ -244,24 +244,29 @@ def print_variations(first_seg,last_seg,feat,paths,seg_seq):
 
 
 def print_current_var(variation,feat_start,list_segfeat_azu,feat,i):
+    warning=detect_small_inversion(variation)
     if variation.type=='insertion':
         [pos_old,pos_new]=get_old_new_pos_insertion(variation,feat_start,list_segfeat_azu,feat)
-        line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tinsertion\t-\t{variation.alt}\t{len(variation.alt)}\t{pos_old}\t{pos_new}\n'
+        line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tinsertion\t-\t{variation.alt}\t{len(variation.alt)}\t{pos_old}\t{pos_new}{warning}\n'
         write_line(line,output_variations,False)
     elif variation.type=='deletion':
         [pos_old,pos_new]=get_old_new_pos_deletion(variation,feat_start,list_segfeat_azu,feat,i)
-        line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tdeletion\t{variation.ref}\t-\t{len(variation.ref)}\t{pos_old}\t{pos_new}\n'
+        line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tdeletion\t{variation.ref}\t-\t{len(variation.ref)}\t{pos_old}\t{pos_new}{warning}\n'
         write_line(line,output_variations,False)
     elif variation.type=='substitution':
-        warning=detect_small_inversion(variation)
         [pos_old,pos_new]=get_old_new_pos_substitution(feat_start,variation,list_segfeat_azu,feat)
-        if len(variation.ref) == len(variation.alt): # if the substituion is between two segment of the same size, print it
-            size_subs=len(variation.ref)
-            line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tsubstitution\t{variation.ref}\t{variation.alt}\t{size_subs}\t{pos_old}\t{pos_new}{warning}\n'
-        else :
-            # if the segments of the substitution have a different size, print deletion then insertion at the same position.
-            line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tdeletion\t{variation.ref}\t-\t{len(variation.ref)}\t{pos_old}\t{pos_new}{warning}\n'
-            line+=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tinsertion\t-\t{variation.alt}\t{len(variation.alt)}\t{pos_old}\t{pos_new}{warning}\n'
+
+        size_subs=len(variation.ref)+"/"+len(variation.alt)
+        line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tsubstitution\t{variation.ref}\t{variation.alt}\t{size_subs}\t{pos_old}\t{pos_new}{warning}\n'
+        
+        # print the substitutions of different size as deletion+insertion.
+        #if len(variation.ref) == len(variation.alt): # if the substituion is between two segment of the same size, print it
+        #    size_subs=len(variation.ref)
+        #    line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tsubstitution\t{variation.ref}\t{variation.alt}\t{size_subs}\t{pos_old}\t{pos_new}{warning}\n'
+        #else :
+        #    # if the segments of the substitution have a different size, print deletion then insertion at the same position.
+        #    line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tdeletion\t{variation.ref}\t-\t{len(variation.ref)}\t{pos_old}\t{pos_new}{warning}\n'
+        #    line+=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tinsertion\t-\t{variation.alt}\t{len(variation.alt)}\t{pos_old}\t{pos_new}{warning}\n'
         write_line(line,output_variations,False)
 
 def detect_small_inversion(variation):