modified the condition for the transfer. now the filters coverage and id only...

modified the condition for the transfer. now the filters coverage and id only apply to genes. if the gene passes the filters, all its child features are transfered. if the gene doesnt pass the filters, none of its child features are transfered

Functions_output.py

-from Graph_gff import Segments, Features, write_line
+from Graph_gff import Segments, Features, write_line, find_parent
 from Functions import *
 
 
@@ -7,26 +7,33 @@ from Functions import *
 
 # functions to get the gff with one line per feature
 # outputs the feature once in a gff, from the first to the last segment present on the new genome (if the size is ok) :
-def generate_target_gff(first_seg,last_seg,feature_id,max_diff,inversion,walk,seg_size,args):
+def generate_target_gff(feature_id,max_diff,seg_size,args,reason_features_not_transfered):
+    feature=Features[feature_id]
+    # get list of the segments where it is and the first and last segment of the feature on the new genome
+    feature_target_path=feature.segments_list_target
+    [first_seg,last_seg,walk]=get_featurePath_ends(feature_target_path)
+    inversion=detect_feature_inversion(feature.segments_list_source,feature_target_path)
 
     if first_seg!='': # feature present on the target genome
         if inversion:
             size_on_new_genome=get_feature_start_on_target_genome_inv(last_seg,feature_id,walk)-get_feature_stop_on_target_genome_inv(first_seg,feature_id,walk)+1
         else:
             size_on_new_genome=get_feature_stop_on_target_genome(last_seg,feature_id,walk)-get_feature_start_on_target_genome(first_seg,feature_id,walk)+1
-        size_diff=abs(size_on_new_genome-Features[feature_id].size)
+        size_diff=abs(size_on_new_genome-feature.size)
         [cov,id]=get_id_cov(feature_id,seg_size)
-        if (cov*100<args.coverage) or (id*100<args.identity):
-            return "cov_id"
-        if right_size(size_on_new_genome,max_diff,feature_id): 
+        if ((cov*100<args.coverage) or (id*100<args.identity)) and (feature.type=="gene"):
+            reason_features_not_transfered[2]+=1
+            return "no"
+        if right_size(size_on_new_genome,max_diff,feature_id) or (feature.type!="gene"): 
             line_gff=create_line_target_gff(first_seg,last_seg,feature_id,size_diff,inversion,walk,cov,id)
             write_line(line_gff,output_target_gff,False)
             return size_diff
         else:
-            return "bad_size"
+            reason_features_not_transfered[0]+=1
+            return "no"
     else :
-        return "absent"
-    # add cov or id too low to reason to not transfer !!
+        reason_features_not_transfered[1]+=1
+        return "no"
 
 
 
@@ -46,33 +53,42 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_aln,target_gen
         file_out=open(out_target_gff,'w')
         global output_target_gff
         output_target_gff=[0,"",file_out]
-        bad_size_features=0
-        absent_features=0
-        cov_id_bad=0
+        reason_features_not_transfered=[0,0,0] # bad_size, absent_features, low_cov_id
         diff_size_transfered_features=[0,0] # [count,sum], to get the average
+        genes_done={} # key=gene_id, value=true if done and passed, and value=false if done but not passed. if not passed, dont transfer child features
 
         for feat in list_feature_to_transfer:
-            # for each feature, get list of the segments where it is and the first and last segment of the feature on the new genome
-            feature_target_path=Features[feat].segments_list_target
-            [first_seg,last_seg,walk]=get_featurePath_ends(feature_target_path)
-            inversion=detect_feature_inversion(Features[feat].segments_list_source,feature_target_path)
-
-            transfer_stat=generate_target_gff(first_seg,last_seg,feat,args.max_difference,inversion,walk,seg_size,args) # insertions not considered !!!
-            if transfer_stat=="bad_size":
-                bad_size_features+=1
-                if Features[feat].type=='gene':
-                    list_feat_absent.append(feat)
-            elif transfer_stat=="absent":
-                absent_features+=1
-                if Features[feat].type=='gene':
-                    list_feat_absent.append(feat)
-            elif transfer_stat=="cov_id":
-                cov_id_bad+=1
-                if Features[feat].type=='gene':
-                    list_feat_absent.append(feat)
-            else:
-                diff_size_transfered_features[0]+=1
-                diff_size_transfered_features[1]+=transfer_stat
+            transfer=True
+            parent=find_parent(feat)
+
+            # do the parent gene then the child feature. dont do a child feature if the gene didnt pass.
+            if parent not in genes_done: # gene parent never seen, transfer it
+                if Features[feat].type!="gene":
+                    transfer_stat=generate_target_gff(parent,args.max_difference,seg_size,args,reason_features_not_transfered)
+                    if transfer_stat=="no":
+                        genes_done[parent]=False
+                        transfer=False
+                        list_feat_absent.append(feat)
+                    else:
+                        diff_size_transfered_features[0]+=1
+                        diff_size_transfered_features[1]+=transfer_stat
+                        genes_done[parent]=True
+            else: # gene parent already transfered
+                if not genes_done[parent]: # the gene parent didnt pass the filters
+                    transfer=False
+                elif Features[feat].type=="gene": # the current feature is the gene and has alrady been transfered
+                    transfer=False
+
+            if transfer==True:
+                transfer_stat=generate_target_gff(feat,args.max_difference,seg_size,args,reason_features_not_transfered) # insertions not considered !!!
+                if transfer_stat=="no":
+                    if Features[feat].type=='gene':
+                        genes_done[feat]=False
+                        list_feat_absent.append(feat)
+                else:
+                    diff_size_transfered_features[0]+=1
+                    diff_size_transfered_features[1]+=transfer_stat
+                    genes_done[feat]=True
 
         write_line("",output_target_gff,True)
         file_out.close()
@@ -144,10 +160,11 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_aln,target_gen
             stats_feature_missing_segment(feature_missing_segments,first_seg,last_seg,list_seg,feat,walk)
 
         if args.annotation:
-            print(len(Features)-(bad_size_features+absent_features+cov_id_bad),"out of",len(Features),"features are transfered.")
+            bad_size_features=reason_features_not_transfered[0];absent_features=reason_features_not_transfered[1];low_cov_id=reason_features_not_transfered[2]
+            print(len(Features)-(bad_size_features+absent_features+low_cov_id),"out of",len(Features),"features are transfered.")
             print(bad_size_features,"out of",len(Features), "features are not transfered because they are too big or too small compared to the original genome.")
             print(absent_features,"out of",len(Features),"features are not transfered because they are absent in the new genome.")
-            print(cov_id_bad,"out of",len(Features),"features are not transfered because their coverage or sequence identity is below threshold.")
+            print(low_cov_id,"out of",len(Features),"features are not transfered because their coverage or sequence identity is below threshold.")
             print("average length difference of the transfered genes : ",diff_size_transfered_features[1]/diff_size_transfered_features[0])
         stats_features(feature_missing_segments)