When renaming contigs for Replicon files, also keep their name and size, to...

When renaming contigs for Replicon files, also keep their name and size, to use to generate gff files

PanACoTA/utils.py

@@ -847,7 +847,7 @@ def check_out_dirs(resdir):
         sys.exit(1)
 
 
-def rename_genome_contigs(gembase_name, gpath, outfile):
+def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
     """
     For the given genome (sequence in gpath), rename all its contigs
     with the new name: 'gembase_name', and save the output sequence in outfile
@@ -863,14 +863,25 @@ def rename_genome_contigs(gembase_name, gpath, outfile):
 
     """
     contig_num = 1
+    cont_size = 0
+    contigs = []
     with open(gpath, "r") as gpf, open(outfile, "w") as grf:
         for line in gpf:
-            if line.startswith(">"):
+            # When we find a new header line, convert its name to gembase format, and write it
+            # to the list of contigs, as well as its size (calculated before)
+            if line.startswith(">") :
                 new_cont = ">" + gembase_name + "." + str(contig_num).zfill(4)
-                contig_num += 1
                 grf.write(new_cont + "\n")
+                # If first contig, just convert its name, but no size yet
+                if cont_size != 0:
+                    contigs.append("{};{}".format(new_cont, cont_size))
+                contig_num += 1
+                cont_size = 0
             else:
                 grf.write(line)
+                cont_size += len(line.strip())
+        contigs.append("{};{}".format(new_cont, cont_size))
+    return contigs
 
 
 def logger_thread(q):