the dict seg_size is now built from the function get_segments_lengths in main

main.py

@@ -54,16 +54,9 @@ if args.annotation or args.variation or args.alignment:
 
     seg_size={}
     if args.annotation:
-        segments_file = open(segments,'r')
-        lines=segments_file.readlines()
-        segments_file.close()
-
-        # build a dictionnary with the segment sizes
-        for line in lines:
-            line=line.split()
-            seg_id='s'+line[1]
-            segment_size=len(line[2])
-            seg_size[seg_id]=segment_size
+        # get a dictionnary with the segment sizes
+        seg_size=get_segments_length(segments)
+
 
     genome_index=0
     for target_genome in args.target: