From 8b91326f9c6eecdc0770792e0fb9dd6be5899450 Mon Sep 17 00:00:00 2001
From: Niko <nikolaos.papadopoulos@univie.ac.at>
Date: Wed, 4 Dec 2024 15:32:23 +0100
Subject: [PATCH] documenting the decision to omit exons from the EMBL file
 this was mostly done to avoid the validator complaint about "abutting exons"
 that are adjacent to each other, a situation underscored by PacBio
 transcripts.

---
 08-submission/gff-04-convert_to_embl.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/08-submission/gff-04-convert_to_embl.sh b/08-submission/gff-04-convert_to_embl.sh
index 8149726..4b39f04 100644
--- a/08-submission/gff-04-convert_to_embl.sh
+++ b/08-submission/gff-04-convert_to_embl.sh
@@ -9,6 +9,9 @@ RESDIR=/lisc/scratch/zoology/pycnogonum/genome/submission
 
 cd $RESDIR || exit
 
+# first run EMBLmyGFF3 --expose-translations
+# and edit translation_gff_feature_to_embl_feature.json to include "remove": true for exons
+
 EMBLmyGFF3 $GFF $GENOME \
         --topology linear \
         --molecule_type 'genomic DNA' \
-- 
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