From 5a3aa67fbdeb65e0b5ffbf239e0d732f44045c93 Mon Sep 17 00:00:00 2001
From: Niko <nikolaos.papadopoulos@univie.ac.at>
Date: Thu, 28 Nov 2024 12:18:13 +0100
Subject: [PATCH] now renaming pseudochromosomes appropriately

---
 08-submission/gff-01-compose_gff.sh | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/08-submission/gff-01-compose_gff.sh b/08-submission/gff-01-compose_gff.sh
index 30f1ce3..c6e0f95 100644
--- a/08-submission/gff-01-compose_gff.sh
+++ b/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
-- 
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