now renaming pseudochromosomes appropriately

08-submission/gff-01-compose_gff.sh

@@ -19,6 +19,14 @@ cd $RESULT || exit
 # merge the GFF3 files
 cat $ISOSEQ $BRAKER_R1 $BRAKER_R2 $DENOVO $TRNASCAN > merged.gff3
 
+# rename pseudochromosomes 54-59 to 52-57 to reflect decontamination
+sed -i 's/pseudochrom_54/pseudochrom_52/g' merged.gff3
+sed -i 's/pseudochrom_55/pseudochrom_53/g' merged.gff3
+sed -i 's/pseudochrom_56/pseudochrom_54/g' merged.gff3
+sed -i 's/pseudochrom_57/pseudochrom_55/g' merged.gff3
+sed -i 's/pseudochrom_58/pseudochrom_56/g' merged.gff3
+sed -i 's/pseudochrom_59/pseudochrom_57/g' merged.gff3
+
 # sort the GFF3 file
 module load genometools/
 gt gff3 -tidy -retainids -o merged_sorted.gff3 -force merged.gff3