From 500a24a6ff29d7d14f23c1b3076584fb5e7eb01a Mon Sep 17 00:00:00 2001
From: Niko <nikolaos.papadopoulos@univie.ac.at>
Date: Wed, 27 Nov 2024 15:55:18 +0100
Subject: [PATCH] sorted out GFF creation

---
 08-submission/gff-01-compose_gff.sh | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/08-submission/gff-01-compose_gff.sh b/08-submission/gff-01-compose_gff.sh
index a2c9b89..30f1ce3 100644
--- a/08-submission/gff-01-compose_gff.sh
+++ b/08-submission/gff-01-compose_gff.sh
@@ -2,22 +2,23 @@
 
 # compose the GFF3 file to prepare for ENA submission
 
-# first gather the various input sources
+# set base and result directory
 BASE=/lisc/scratch/zoology/pycnogonum/genome/draft/annot_merge
+RESULT=/lisc/scratch/zoology/pycnogonum/genome/submission
+
+# first gather the various input sources
 ISOSEQ=$BASE/isoseq.gff
 BRAKER_R1=$BASE/braker.gff
 BRAKER_R2=$BASE/braker2_unique_renamed_nocodon_intron.gff3
-DENOVO=$BASE/overlap_translated.gff3
+DENOVO=$BASE/denovo_txomes/overlap_translated.gff3
+TRNASCAN=$BASE/../trnascan/trnascan.gff3
+
+# navigate to output directory
+cd $RESULT || exit
 
-ls ISOSEQ
-ls BRAKER_R1
-ls BRAKER_R2
-ls DENOVO
+# merge the GFF3 files
+cat $ISOSEQ $BRAKER_R1 $BRAKER_R2 $DENOVO $TRNASCAN > merged.gff3
 
-# cat isoseq.gff > merged.gff3
-# cat braker.gff >> merged.gff3
-# cat braker2_unique_renamed_nocodon_intron.gff3 >> merged.gff3
-# cat denovo_txomes/overlap_translated.gff3 >> merged.gff3
-# cat ../trnascan/trnascan.gff3 >> merged.gff3
-# module load genometools/
-# gt gff3 -tidy -retainids -o merged_sorted.gff3 -force merged.gff3
\ No newline at end of file
+# sort the GFF3 file
+module load genometools/
+gt gff3 -tidy -retainids -o merged_sorted.gff3 -force merged.gff3
-- 
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