changed the way to get the list of features to transfer

Functions_output.py

@@ -51,7 +51,7 @@ def gff_one(first_seg,last_seg,feature_id,list_seg,max_diff):
 
 
 # writes the gff of azucena using the gff of the graph
-def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var,target_genome_name,max_diff):
+def genome_gff(pos_seg, gfa, out_once, out_detail, out_var,target_genome_name,max_diff):
     print("generation of the genome's gff ")
 
     # create variables and open files
@@ -83,7 +83,7 @@ def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var,target_genome_na
         # no segment is missing, the feature is complete - feature_ok  
         # total number of features, with missing segments or not - feature_total
     get_segments_positions_on_genome(pos_seg)
-    list_feature_to_transfer=get_all_features_in_gff(gff) # get the list of all the features to transfer from the gff
+    list_feature_to_transfer= Features.keys()
 
     for feat in list_feature_to_transfer:
 

main.py

@@ -43,7 +43,7 @@ if run=="command_line":
 
     # outputs the gff of a genome for the chr10
     max_diff=2 # maximum size difference (n times bigger or smaller) between the gene on the reference genome and the gene on the target genome for the gene to be transfered.
-    genome_gff(pos_seg,out_gff,gfa,out_once,out_detail,out_var,target_genome_name,max_diff)
+    genome_gff(pos_seg,gfa,out_once,out_detail,out_var,target_genome_name,max_diff)