adapted the code to the changes made to handle several chromosomes

Graph_gff.py

@@ -206,12 +206,12 @@ def graph_gff(graph_gff_file):
 
     graph_gff_file.close()
 
-def graph_gaf(graph_gaf_file,gfa_file):
+def graph_gaf(graph_gaf_file,segments_file):
     print("generation of the graph's gaf")
     graph_gaf_file = open(graph_gaf_file, 'w')
     output_graph_gaf[2]=graph_gaf_file
 
-    seg_len=get_segments_length(gfa_file)
+    seg_len=get_segments_length(segments_file)
     for feature_id in Features:
         feature=Features[feature_id]
         feature_segments=feature.segments_list_source
@@ -231,22 +231,14 @@ def graph_gaf(graph_gaf_file,gfa_file):
 
     graph_gaf_file.close()
 
-
-
-
-
 def get_segments_length(gfa):
     file_gfa=open(gfa,'r')
     lines_gfa=file_gfa.readlines()
     file_gfa.close()
     seg_len={}
-    segment_encountered=False
     for line in lines_gfa:
         line=line.split()
         if (line[0]=="S"): # get the length of the segment
-            segment_encountered=True
             seg_id='s'+line[1]
             seg_len[seg_id]=len(line[2])
-        elif segment_encountered==True: # so we don't have to go through all the L lines. once we found one S, if we find something else than S it stops
-            return seg_len
     return seg_len
\ No newline at end of file