changed how the inversion info is passed

Functions.py

@@ -46,7 +46,7 @@ def create_line_target_gff(first_seg,last_seg,feature_id,size_diff,inversion):
     var_count=count_variations(feature_id)
     annotation=f'{feature.annot};Size_diff={size_diff};Nb_variants={var_count}'
 
-    if inversion=='1':
+    if inversion:
         start=get_feature_start_on_target_genome_inv(last_seg,feature_id)
         stop=get_feature_stop_on_target_genome_inv(first_seg,feature_id)
         strand=invert_strand(strand)
@@ -344,22 +344,6 @@ def get_first_seg(list_seg): # get the first segment of the list that is in the
 
 # functions to get the detail of the variations in the features
 
-def compare_strand(list_1,list_2,list_1_unstrand,list_2_unstrand):
-    # get the list of segments in common
-    seg_common=[]
-    for segment in list_1_unstrand:
-        if segment in list_2_unstrand:
-            seg_common.append(segment)
-
-    # for each segment in common, check if the strand is the same. check index in list unstranded to get the segment in list stranded
-    same_strand_count=0
-    for segment in seg_common:
-        index_1=list_1_unstrand.index(segment)
-        index_2=list_2_unstrand.index(segment)
-        if list_1[index_1]==list_2[index_2]:
-            same_strand_count+=1
-    return [seg_common,same_strand_count]
-
 # find on what target path the segments of the feature are (ie what chromosome/contig)
 def find_feature_target_path(first_seg,last_seg,target_genome_paths):
     feature="not_found"
@@ -407,7 +391,7 @@ def count_variations(feature_id):
     if len(target_list)!=0:
         source_list=feature.segments_list_source
         inversion=detect_feature_inversion(source_list,target_list)
-        if inversion=="1":
+        if inversion:
             target_list=invert_segment_list(target_list)
         target_dict=dict.fromkeys(target_list,"")
         source_dict=dict.fromkeys(source_list,"") # convert list into dict to search segments in dict quicker.
@@ -495,7 +479,7 @@ def create_var(feature_id,first_seg,last_seg):
     feature_path_source_genome=feature.segments_list_source
     inversion=detect_feature_inversion(feature_path_source_genome,feature_path_target_genome)
 
-    if inversion=="1":
+    if inversion:
         feature_path_target_genome=invert_segment_list(feature_path_target_genome)
         start_new_genome=get_feature_start_on_target_genome_inv(last_seg,feature_id)
         stop_new_genome=get_feature_stop_on_target_genome_inv(first_seg,feature_id)
@@ -525,7 +509,7 @@ def get_old_new_pos_substitution(feat_start,variation,feature_path_target_genome
 
     start_feat_seg=feature_path_target_genome[0]
     var_start_seg=variation.start_on_target
-    if variation.inversion=='1':
+    if variation.inversion:
         start_feat_seg=invert_seg(start_feat_seg)
         var_start_seg=invert_seg(var_start_seg)
         end_var=segments_on_target_genome[var_start_seg][2]
@@ -543,7 +527,7 @@ def get_old_new_pos_insertion(variation,feat_start,feature_path_target_genome,fe
 
     start_feat_seg=feature_path_target_genome[0]
     start_var_seg=variation.start_var
-    if variation.inversion=='1':
+    if variation.inversion:
         start_feat_seg=invert_seg(start_feat_seg)
         start_var_seg=invert_seg(start_var_seg)
         end_var=segments_on_target_genome[start_var_seg][2]+len(variation.alt) # start_var_seg is the segment AFTER the insertion
@@ -571,7 +555,7 @@ def get_old_new_pos_deletion(variation,feat_start,feature_path_target_genome,fea
     else:
         start_feat_seg=feature_path_target_genome[0]
         start_var_seg=variation.last_seg_in_target
-        if variation.inversion=='1':
+        if variation.inversion:
             start_feat_seg=invert_seg(start_feat_seg)
             start_var_seg=invert_seg(start_var_seg)
             start_var=segments_on_target_genome[start_var_seg][1]-1
@@ -637,6 +621,22 @@ def get_common_segments(list1,list2):
             list_output.append(elem)
     return list_output
 
+def compare_strand(list_1,list_2,list_1_unstrand,list_2_unstrand):
+    # get the list of segments in common
+    seg_common=[]
+    for segment in list_1_unstrand:
+        if segment in list_2_unstrand:
+            seg_common.append(segment)
+
+    # for each segment in common, check if the strand is the same. check index in list unstranded to get the segment in list stranded
+    same_strand_count=0
+    for segment in seg_common:
+        index_1=list_1_unstrand.index(segment)
+        index_2=list_2_unstrand.index(segment)
+        if list_1[index_1]==list_2[index_2]:
+            same_strand_count+=1
+    return [seg_common,same_strand_count]
+
 def detect_segment_order_inversion(list_1,list_2):
     if (len(list_1)==1) | (len(list_2)==1):
         return False
@@ -664,6 +664,8 @@ def detect_orient_inversion(list_1,list_2):
 
 # takes two lists of segments for two genes, check if the first list is an inversion of the second one (if the segments in common are on the opposite strand)
 def detect_feature_inversion(list_1,list_2):
+#    target_dict=dict.fromkeys(target_list,"")
+ 
     # check if we have an inversion of the orientation of the segments
     [strand_inversion,list_1_unstrand,list_2_unstrand]=detect_orient_inversion(list_1,list_2)
 
@@ -672,12 +674,9 @@ def detect_feature_inversion(list_1,list_2):
 
     # if there we have both inversions, the gene is in an inverted region. reverse the second list for the comparison.
     if segment_order_inversion & strand_inversion:
-        inversion=1
-        list_2=invert_segment_list(list_2)
+        return True
     else :
-        inversion=0
-
-    return str(inversion)
+        return False
 
 def invert_segment_list(seg_list):
     list_inverted=list()

Functions_output.py

@@ -151,7 +151,7 @@ def print_alignment(first_seg,feat,seg_seq):
         feature_path_target_genome=feature.segments_list_target
         feature_path_source_genome=feature.segments_list_source
         inversion=detect_feature_inversion(feature_path_source_genome,feature_path_target_genome)
-        if inversion=="1":
+        if inversion:
             feature_path_target_genome=invert_segment_list(feature_path_target_genome)
 
         line_aln=create_line_aln(feature_path_source_genome,feature_path_target_genome,seg_seq,feat)
@@ -266,27 +266,27 @@ def print_current_var(variation,feat_start,feature_path_target_genome,feat):
     warning=''
     if variation.type=='insertion':
         [pos_old,pos_new]=get_old_new_pos_insertion(variation,feat_start,feature_path_target_genome,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}{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{print_inversion(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,feature_path_target_genome,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}\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{print_inversion(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,feature_path_target_genome,feat)
 
         size_subs=f'{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'
+        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{print_inversion(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'
+        #    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{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'
+        #    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{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{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):
@@ -314,13 +314,23 @@ def print_last_deletion(variation,feature_path_source_genome,i,feat_start,featur
     length=len(del_sequence)
     pos_new=str(int(variation.size_new)+1) # the deletion is at the end of the feature on the new genome
 
-    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{del_sequence}\t-\t{length}\t{pos_old}\t{pos_new}\n'
+    if variation.inversion:
+        inversion='1'
+    else:
+        inversion='0'
+
+    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{inversion}\t{variation.size_diff}\tdeletion\t{del_sequence}\t-\t{length}\t{pos_old}\t{pos_new}\n'
     write_line(line,output_variations,False)
 
 def print_novar(variation):
-    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}\tno_var\t-\t-\t-\t-\t-\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{print_inversion(variation.inversion)}\t{variation.size_diff}\tno_var\t-\t-\t-\t-\t-\n'
     write_line(line,output_variations,False)
 
+def print_inversion(bool):
+    if bool==True:
+        return '1'
+    else:
+        return '0'
 
 # not used.