the dict segments_on_target_genome now stores the segment twice if it is...

the dict segments_on_target_genome now stores the segment twice if it is present twice in a given walk. adapted the rest of the code to use the last occurence (like before, will change that later)

Functions.py

@@ -5,30 +5,42 @@ segments_on_target_genome={}
 
 # get the start position of the features on the linear genome, using their coordinates on the graph and the coordinantes of the segments on the genome
 def get_feature_start_on_target_genome(start_seg,feat_id,walk):
-    seg_start_pos=segments_on_target_genome[start_seg][walk][1]
+    seg_start_pos=segments_on_target_genome[start_seg][walk][-1][1]
     feat_start_pos=get_feature_start_on_segment(start_seg,feat_id)
+
+    if len(segments_on_target_genome[start_seg][walk])>1:
+        print("*** several start_seg found ",start_seg)
     
     return seg_start_pos+feat_start_pos-1
 
 # get the stop position of the features on the linear genome, using their coordinates on the graph and the coordinantes of the segments on the genome
 def get_feature_stop_on_target_genome(stop_seg,feat_id,walk):
-    seg_start_pos=segments_on_target_genome[stop_seg][walk][1]
+    seg_start_pos=segments_on_target_genome[stop_seg][walk][-1][1]
     feat_stop_pos=get_feature_stop_on_segment(stop_seg,feat_id)
+
+    if len(segments_on_target_genome[stop_seg][walk])>1:
+        print("*** several stop_seg found ",stop_seg)
     
     return seg_start_pos+feat_stop_pos-1
 
 
 # get the start position of the features on the linear genome for inverted features
 def get_feature_start_on_target_genome_inv(start_seg,feat_id,walk):
-    seg_end_pos=segments_on_target_genome[start_seg][walk][2]
+    seg_end_pos=segments_on_target_genome[start_seg][walk][-1][2]
     feat_start_pos=get_feature_start_on_segment(start_seg,feat_id)
 
+    if len(segments_on_target_genome[start_seg][walk])>1:
+        print("*** several start_seg found ",start_seg)
+
     return seg_end_pos-feat_start_pos+1
 
 # get the stop position of the features on the linear genome for inverted features
 def get_feature_stop_on_target_genome_inv(stop_seg,feat_id,walk):
-    seg_end_pos=segments_on_target_genome[stop_seg][walk][2]
+    seg_end_pos=segments_on_target_genome[stop_seg][walk][-1][2]
     feat_stop_pos=get_feature_stop_on_segment(stop_seg,feat_id)
+
+    if len(segments_on_target_genome[stop_seg][walk])>1:
+        print("*** several stop_seg found ",stop_seg)
     
     return seg_end_pos-feat_stop_pos+1
 
@@ -41,7 +53,7 @@ def right_size(size,max_diff,feat):
     return not ((size>Features[feat].size*max_diff) or (size<Features[feat].size/max_diff)) 
 
 def create_line_target_gff(first_seg,last_seg,feature_id,size_diff,inversion,walk,cov,id):
-    [chr,strand,feature]=[segments_on_target_genome[first_seg][walk][0],Features[feature_id].strand,Features[feature_id]]
+    [chr,strand,feature]=[segments_on_target_genome[first_seg][walk][-1][0],Features[feature_id].strand,Features[feature_id]]
 
     annotation=f'{feature.annot};Size_diff={size_diff};coverage={cov};sequence_ID={id}' # Nb_variants={var_count};
 
@@ -289,7 +301,11 @@ def get_segments_positions_on_genome(pos_seg): # add to the dict the info about
         #segments_on_target_genome[seg]=[chrom,start,stop,strand,index,file_name]
         if seg not in segments_on_target_genome:
             segments_on_target_genome[seg]={} # dict of walks->segment_info; you get the info about the segment for each walk
-        segments_on_target_genome[seg][file_name]=[chrom,start,stop,strand,index]
+        if file_name not in segments_on_target_genome[seg]:
+            segments_on_target_genome[seg][file_name]=list()
+        else:
+            print("doublon",file_name,seg)
+        segments_on_target_genome[seg][file_name].append([chrom,start,stop,strand,index])
         seg_count+=1
 
 # look for the segment on either strand of the target genome
@@ -375,10 +391,15 @@ def add_target_genome_path(feature_id,target_genome_paths):
 
 # find the feature's path in target genome
 def get_feature_path(target_genome_path,first_seg,last_seg,walk_name):
-    #first_seg=search_seg_on_target_genome(first_seg)
-    #last_seg=search_seg_on_target_genome(last_seg)
-    first_seg_index=segments_on_target_genome[first_seg][walk_name][4]
-    last_seg_index=segments_on_target_genome[last_seg][walk_name][4]
+    # si on a plusieurs occurences de first_seg et last_seg, ???
+    # prendre la dernière et print qu'il y en a d'autre.
+    if len(segments_on_target_genome[first_seg][walk_name])>1:
+        print("*** several first_seg found ",first_seg)
+    if len(segments_on_target_genome[last_seg][walk_name])>1:
+        print("*** several last_seg found ",last_seg)
+    
+    first_seg_index=segments_on_target_genome[first_seg][walk_name][-1][4]
+    last_seg_index=segments_on_target_genome[last_seg][walk_name][-1][4]
     first_index=min(first_seg_index,last_seg_index)
     last_index=max(first_seg_index,last_seg_index)
     feature_path_target_genome=target_genome_path[first_index:last_index+1]
@@ -568,7 +589,7 @@ def create_var(feature_id,first_seg,last_seg,walk):
         stop_new_genome=get_feature_stop_on_target_genome(last_seg,feature_id,walk)
         size_new_genome=stop_new_genome-start_new_genome+1
     size_diff=str(size_new_genome-feature.size)
-    sequence_name=segments_on_target_genome[first_seg][walk][0]
+    sequence_name=segments_on_target_genome[first_seg][walk][-1][0]
 
     variation=Variation(feature_id,feature.type,sequence_name,start_new_genome,stop_new_genome,inversion,size_diff,size_new_genome)
     return(variation,feature_path_source_genome,feature_path_target_genome)
@@ -590,11 +611,11 @@ def get_old_new_pos_substitution(feat_start,variation,start_feat_seg_target,feat
     if variation.inversion:
         start_feat_seg_target=invert_seg(start_feat_seg_target)
         var_start_seg=invert_seg(var_start_seg)
-        end_var=segments_on_target_genome[var_start_seg][walk][2]
+        end_var=segments_on_target_genome[var_start_seg][walk][-1][2]
         start_feat=get_feature_start_on_target_genome_inv(start_feat_seg_target,feat,walk)
         pos_new=str(start_feat-end_var)
     else:
-        start_var=segments_on_target_genome[var_start_seg][walk][1]
+        start_var=segments_on_target_genome[var_start_seg][walk][-1][1]
         start_feat=get_feature_start_on_target_genome(start_feat_seg_target,feat,walk)
         pos_new=str(start_var-start_feat)
     return [pos_old,pos_new] # pos_old and pos_new are the base before the change
@@ -607,11 +628,11 @@ def get_old_new_pos_insertion(variation,feat_start,start_feat_seg_target,feat,wa
     if variation.inversion:
         start_feat_seg_target=invert_seg(start_feat_seg_target)
         start_var_seg=invert_seg(start_var_seg)
-        end_var=segments_on_target_genome[start_var_seg][walk][2]+len(variation.alt) # start_var_seg is the segment AFTER the insertion
+        end_var=segments_on_target_genome[start_var_seg][walk][-1][2]+len(variation.alt) # start_var_seg is the segment AFTER the insertion
         start_feat=get_feature_start_on_target_genome_inv(start_feat_seg_target,feat,walk) 
         pos_new=str(start_feat-end_var)
     else:
-        start_var=segments_on_target_genome[start_var_seg][walk][1]-len(variation.alt) # start_var_seg is the segment AFTER the insertion
+        start_var=segments_on_target_genome[start_var_seg][walk][-1][1]-len(variation.alt) # start_var_seg is the segment AFTER the insertion
         start_feat=get_feature_start_on_target_genome(start_feat_seg_target,feat,walk) 
         pos_new=str(start_var-start_feat)
     return [pos_old,pos_new] # pos_old and pos_new are the base before the change
@@ -634,11 +655,11 @@ def get_old_new_pos_deletion(variation,feat_start,start_feat_seg_target,feat,wal
         if variation.inversion:
             start_feat_seg_target=invert_seg(start_feat_seg_target)
             start_var_seg=invert_seg(start_var_seg)
-            start_var=segments_on_target_genome[start_var_seg][walk][1]-1
+            start_var=segments_on_target_genome[start_var_seg][walk][-1][1]-1
             start_feat=get_feature_start_on_target_genome_inv(start_feat_seg_target,feat,walk) 
             pos_new=str(start_feat-start_var)
         else:
-            start_var=segments_on_target_genome[start_var_seg][walk][2]+1
+            start_var=segments_on_target_genome[start_var_seg][walk][-1][2]+1
             start_feat=get_feature_start_on_target_genome(start_feat_seg_target,feat,walk)
             pos_new=str(start_var-start_feat)
     return [pos_old,pos_new] # pos_old and pos_new are the base before the change