changed the detection of the target genome path in which each feature is

Functions.py

@@ -243,10 +243,11 @@ def get_segments_positions_on_genome(pos_seg):
     seg_count=0
     for line in lines:
         line=line.split()
+        file_name='.'.join(pos_seg.split('/')[-1].split('.')[0:-1])
         [seg,chrom,start,stop,strand,index]=[line[3][1:],line[0],int(line[1])+1,int(line[2]),line[3][0:1],seg_count] # +1 in the start to convert the bed 0-based coordinate to a 1-based system
         # if seg in segments_on_target_genome:
         #     print("seg already present on target genome")
-        segments_on_target_genome[seg]=[chrom,start,stop,strand,index]
+        segments_on_target_genome[seg]=[chrom,start,stop,strand,index,file_name]
         seg_count+=1
 
 def get_segments_sequence(segments_file,segments_list):
@@ -283,7 +284,7 @@ def get_first_seg(list_seg): # get the first segment of the list that is in the
     first_seg_found=''
     for segment in list_seg:
         if segment[1:] in segments_on_target_genome:
-            first_seg_found=segment[1:]
+            first_seg_found=segment
             break
     return first_seg_found
 
@@ -306,29 +307,34 @@ def compare_strand(list_1,list_2,list_1_unstrand,list_2_unstrand):
             same_strand_count+=1
     return [seg_common,same_strand_count]
 
-def get_chr_path(feature_id,target_genome_paths):
-    feat_chr_number=Features[feature_id].chr[3:]
-    for path_name in target_genome_paths.keys():
-        if feat_chr_number in path_name[-3:]:
-            return target_genome_paths[path_name]
-    return False
+def find_feature_target_path(first_seg,last_seg,target_genome_paths):
+    feature="not_found"
+    path_first_seg=segments_on_target_genome[first_seg[1:]][5]
+    path_last_seg=segments_on_target_genome[last_seg[1:]][5]
+    if path_first_seg==path_last_seg:
+        for path in target_genome_paths:
+            if path in path_first_seg:
+                return path
+    return feature
 
 def add_target_genome_path(feature_id,target_genome_paths):
-    target_genome_path=get_chr_path(feature_id,target_genome_paths)
-    if target_genome_path!=False:
-        feature=Features[feature_id]
-        list_seg=feature.segments_list_source
-        first_seg=get_first_seg(list_seg)
-        last_seg=get_first_seg(reversed(list_seg))
-        feature_path=[]
-        if first_seg!='':
-            feature_path=get_feature_path(target_genome_path,first_seg,last_seg)
-        feature.segments_list_target=feature_path
+    feature=Features[feature_id]
+    list_seg=feature.segments_list_source
+    first_seg=get_first_seg(list_seg)
+    last_seg=get_first_seg(reversed(list_seg))
+    feature_path=[]
+    if first_seg!='':
+        path=find_feature_target_path(first_seg,last_seg,target_genome_paths)
+        if path=="frag":
+            print(f'feature {feature_id} fragmented')
+        elif path!="not_found":
+            feature_path=get_feature_path(target_genome_paths[path],first_seg,last_seg)
+    feature.segments_list_target=feature_path
 
 def get_feature_path(target_genome_path,first_seg,last_seg):
     # find the path in target genome
-    first_seg_index=segments_on_target_genome[first_seg][4]
-    last_seg_index=segments_on_target_genome[last_seg][4]
+    first_seg_index=segments_on_target_genome[first_seg[1:]][4]
+    last_seg_index=segments_on_target_genome[last_seg[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]