--- a/RepEnrich_setup.py	Sat Apr 20 12:13:52 2024 +0000
+++ b/RepEnrich_setup.py	Sun Apr 21 09:44:51 2024 +0000
@@ -71,7 +71,7 @@
 genome = defaultdict(dict)
 
 for chr in g.keys():
-    genome[chr]['sequence'] = g[chr].seq
+    genome[chr]['sequence'] = str(g[chr].seq)
     genome[chr]['length'] = len(g[chr].seq)
 
 # Build a bedfile of repeatcoordinates to use by RepEnrich region_sorter
@@ -100,7 +100,7 @@
 
 # generate metagenomes and save them to FASTA files for bowtie build
 for repname in rep_coords:
-    metagenome = ''
+    genomes_list = []
     # iterating coordinate list by block of 3 (chr, start, end)
     block = 3
     for i in range(0, len(rep_coords[repname]) - block + 1, block):
@@ -109,11 +109,8 @@
         start = max(int(batch[1]) - flankingl, 0)
         end = min(int(batch[2]) + flankingl,
                   int(genome[chromosome]['length'])-1) + 1
-        metagenome = (
-            f"{metagenome}{spacer}"
-            f"{genome[chromosome]['sequence'][start:end]}"
-            )
-
+        genomes_list.append(genome[chromosome]['sequence'][start:end])
+    metagenome = spacer.join(genomes_list)
     # Create Fasta of repeat pseudogenome
     fastafilename = f"{repname}.fa"
     record = SeqRecord(Seq(metagenome), id=repname, name='', description='')