sorted out GFF creation

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
+# sort the GFF3 file
+module load genometools/
+gt gff3 -tidy -retainids -o merged_sorted.gff3 -force merged.gff3
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