adapted the code to handle paths without the assembly name, and to output in...

adapted the code to handle paths without the assembly name, and to output in batch to reduce the number of file access

getSegmentsCoordinates.py

 import subprocess
+from Graph_gff import write_line
 
 def has_numbers(inputString):
     return any(char.isdigit() for char in inputString)
@@ -65,9 +66,9 @@ def seg_coord(gfa,walk_names):
     file_names=list()
     for line in lines :
         line=line.split()
-        name=line[3]
+        name=line[1]+"_"+line[3]
 
-        if check_walk_name(walk_names,name) | (len(walk_names)==1): # len=1 if there is only the source genome.
+        if (check_walk_name(walk_names,name)) | ((len(walk_names)==1) & ("MINIGRAPH" not in name)): # len=1 if there is only the source genome.
 
             path_start=int(line[4])
             seq_name=name.split('_')[-1]
@@ -83,25 +84,24 @@ def seg_coord(gfa,walk_names):
                 out_bed = open(file_name, 'w')
             else :
                 out_bed = open(file_name, 'a')
-                
+            output_bed=[0,"",out_bed]
+
             path=line[6].split(',')
             position=path_start
             
             for i in range(1, len(path)): # for each segment in the path, write the position of the segment in the output bed file
                 # coordinates calculation : start=position, stop=position+segment_size-1, then position+=segment_size
-                
+
                 seg_start=position
                 seg_name='s'+path[i][1:]
                 seg_stop=position+segments_size[seg_name]
-            
+
                 out_line=seq_name+'\t'+str(seg_start)+'\t'+str(seg_stop)+'\t'+path[i][0:1]+seg_name+'\n'
-                out_bed.write(out_line)
-                
+                write_line(out_line,output_bed,False)
+
                 position+=segments_size[seg_name]
+            write_line("",output_bed,True)
             out_bed.close()
     
     command="rm seg_coord/segments.txt && rm seg_coord/walks.txt"
-    subprocess.run(command,shell=True,timeout=None)
-
-    command="if ls test/*_MINIGRAPH_* 1> /dev/null 2>&1; then mkdir seg_coord/minigraph_segments && mv *_MINIGRAPH_* seg_coord/minigraph_segments/; fi"
     subprocess.run(command,shell=True,timeout=None)
\ No newline at end of file