added messages to track progress, and reorganised the order of input file reading

main.py

@@ -39,6 +39,7 @@ if len(args.target)==0:
 
 for target_genome in args.target:
     segments_on_target_genome={}
+    print(f'{target_genome} transfer :')
     # create directory to store output files
     command="mkdir "+target_genome
     subprocess.run(command,shell=True,timeout=None)
@@ -46,11 +47,13 @@ for target_genome in args.target:
     # create dictonaries with paths and segments positions.
     for file in segment_coord_files:
         genome_name=get_genome_name(args.target,file)
-        if genome_name!="" :
+        if genome_name!='':#==target_genome :
+            print(f'    loading the information from the file {file}')
             file_path=args.segment_coordinates_path+file
             get_segments_positions_on_genome(file_path)
-            walks_path=args.segment_coordinates_path+"/walks.txt"
-            target_genome_paths=get_paths(walks_path,target_genome)
+    print(f'    loading the walks for the genome {target_genome}')
+    walks_path=args.segment_coordinates_path+"/walks.txt"
+    target_genome_paths=get_paths(walks_path,target_genome)
 
     out_target_gff=target_genome+"/"+target_genome+".gff"
     out_target_var=target_genome+"/"+target_genome+"_var.txt"