removed functions for path indexing and binary search

Functions.py

@@ -253,7 +253,6 @@ def get_segments_sequence_and_paths(gfa,genomes_to_index):
     file_gfa.close()
     seg_seq={}
     paths={}
-    paths_index={}
     for line in lines_gfa:
         line=line.split()
         if (line[0]=="S"): # get the sequence of the segment
@@ -267,22 +266,15 @@ def get_segments_sequence_and_paths(gfa,genomes_to_index):
                 path=line[6].replace(">",";>")
                 path=path.replace("<",";<").split(';')
                 list_segments=[]
-                #list_index=[]
-                #index=0
                 for segment in path:
                     if segment[0:1]=='>':
                         list_segments.append('>s'+segment[1:])
                     elif segment[0:1]=='<':
                         list_segments.append('<s'+segment[1:])
-                    #list_index.append(index)
-                    #index+=1
-                
-                #zipped_lists=zip(list_segments,list_index)
-                #sorted_pairs=sorted(zipped_lists,key=key_segment)
-                #paths_index[line[3]]=list(sorted_pairs)
+
                 paths[line[3]]=list_segments
 
-    return [paths,paths_index,seg_seq]
+    return [paths,seg_seq]
 
 def get_first_seg(list_seg): # get the first segment of the list that is in the target genome
     first_seg_found=''
@@ -311,44 +303,8 @@ def compare_strand(list_1,list_2,list_1_unstrand,list_2_unstrand):
             same_strand_count+=1
     return [seg_common,same_strand_count]
 
-def key_segment(pair):
-    return int(pair[0][2:])
-
-def path_binary_search(indexed_path,segment): # add the option to use the strand or not. rn the strand is not used. it will complicate the comparisons.
-    index=-1
-    if len(indexed_path)==0:
-        print("empty path")
-        return index
-    [found,lower,upper]=[False,0,len(indexed_path)]
-    check_index=(upper+lower)//2        
-    
-    while found==False:
-
-        if upper-lower<=1:
-            if int(indexed_path[check_index][0][2:])==int(segment[2:]):
-                index=indexed_path[check_index][1]
-            break
-
-        if int(segment[2:])==int(indexed_path[check_index][0][2:]):
-            index=indexed_path[check_index][1]
-            found=True
-        elif int(segment[2:])>int(indexed_path[check_index][0][2:]):
-            lower=check_index+1
-            check_index=(upper+lower)//2
-        else:
-            upper=check_index
-            check_index=(upper+lower)//2
-
-    return index
-
-def get_feature_path_binary(target_genome_path_index,target_genome_path,first_seg,last_seg):
+def get_feature_path(target_genome_path,first_seg,last_seg):
     # find the path in target genome
-    first_strand=segments_on_target_genome[first_seg][3]
-    first_seg_stranded=first_strand+first_seg
-    last_strand=segments_on_target_genome[last_seg][3]
-    last_seg_stranded=last_strand+last_seg
-    #first_seg_index=path_binary_search(target_genome_path_index,first_seg_stranded)
-    #last_seg_index=path_binary_search(target_genome_path_index,last_seg_stranded)
     first_seg_index=segments_on_target_genome[first_seg][4]
     last_seg_index=segments_on_target_genome[last_seg][4]
     first_index=min(first_seg_index,last_seg_index)
@@ -422,7 +378,7 @@ class Variation:
     #def __str__(self):
     #    return f"id={self.id}, position on the original genome={self.chr}:{self.start}-{self.stop}, size={self.size}, features={self.features}"
 
-def create_var(feature_id,first_seg,last_seg,target_genome_path,target_genome_path_index):
+def create_var(feature_id,first_seg,last_seg,target_genome_path):
     feature=Features[feature_id]
     start_new_genome=get_feature_start_on_target_genome(first_seg,feature_id)-1
     stop_new_genome=get_feature_stop_on_target_genome(last_seg,feature_id)
@@ -430,7 +386,7 @@ def create_var(feature_id,first_seg,last_seg,target_genome_path,target_genome_pa
     size_diff=str(size_new_genome-feature.size)
 
     # get feature paths on the original genome and on the target genome
-    feature_path_target_genome=get_feature_path_binary(target_genome_path_index,target_genome_path,first_seg,last_seg)
+    feature_path_target_genome=get_feature_path(target_genome_path,first_seg,last_seg)
     feature_path_source_genome=feature.segments_list
     [feature_path_source_genome,feature_path_target_genome,inversion]=detect_feature_inversion(feature_path_source_genome,feature_path_target_genome)
     variation=Variation(feature_id,feature.type,feature.chr,start_new_genome,stop_new_genome,inversion,size_diff,size_new_genome)

Functions_output.py

@@ -31,9 +31,8 @@ def transfer_on_target(pos_seg, gfa, out_once, out_var,out_clustal,target_genome
     [once,var,stats,clustal]=[True,True,False,True]
     genomes_to_index=[target_genome_name]
     if var:
-        [paths,paths_index,seg_seq]=get_segments_sequence_and_paths(gfa,genomes_to_index)
+        [paths,seg_seq]=get_segments_sequence_and_paths(gfa,genomes_to_index)
         target_genome_path=paths[target_genome_name]
-        target_genome_path_index=''#paths_index[target_genome_name]
         file_out_var = open(out_var, 'w')
         global output_variations
         output_variations=[0,"",file_out_var]
@@ -84,7 +83,7 @@ def transfer_on_target(pos_seg, gfa, out_once, out_var,out_clustal,target_genome
 
         # outputs the detail of variations of the feature :
         if var:
-            print_variations(first_seg,last_seg,feat,target_genome_path,target_genome_path_index,seg_seq)
+            print_variations(first_seg,last_seg,feat,target_genome_path,seg_seq)
             write_line("",output_variations,True)
 
         if stats==True:
@@ -111,10 +110,10 @@ def transfer_on_target(pos_seg, gfa, out_once, out_var,out_clustal,target_genome
 
 # functions to get the detail of the variations in the features
 
-def print_variations(first_seg,last_seg,feat,target_genome_path,target_genome_path_index,seg_seq):
+def print_variations(first_seg,last_seg,feat,target_genome_path,seg_seq):
 
     if (first_seg!=''): # if the feature is not completly absent        # add the else, output absent features
-        [variation,feature_path_source_genome,feature_path_target_genome]=create_var(feat,first_seg,last_seg,target_genome_path,target_genome_path_index) # removes the strands in the segment lists
+        [variation,feature_path_source_genome,feature_path_target_genome]=create_var(feat,first_seg,last_seg,target_genome_path) # removes the strands in the segment lists
         feature=Features[feat]
         feat_start=feature.start
         # loop to go through both paths with i and j