Add Vercel configuration for rewrites and build settings

99.scripts/workflow/transcripts_assembly/04.longest_cds_rename.sh

@@ -0,0 +1,25 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <input_dir> <output_dir> <extension>"
+    echo "Extract longest isoform per gene and rename sequences"
+    exit 1
+fi
+
+indir=$1
+outdir=$2
+ext=$3
+
+mkdir -p "$outdir"
+# Process each file in the input directory with the specified extension
+for td_cds in "$indir"/*."$ext"; do
+    stem=$(basename "$td_cds" ."$ext")
+    echo "Processing $td_cds($stem) ..."
+    echo "perl $SCRIPTS/trinity_utils/util/misc/get_longest_isoform_seq_per_trinity_gene.pl $td_cds > $outdir/$stem.longest_isoform.fa"
+    perl "$SCRIPTS"/trinity_utils/util/misc/get_longest_isoform_seq_per_trinity_gene.pl "$td_cds" >"$outdir"/"$stem".longest_isoform.fa
+    echo "$SCRIPTS/rename_trinity_fasta.py $outdir/$stem.longest_isoform.fa $stem $outdir/$stem.full_cds.fa"
+    "$SCRIPTS"/miscs/rename_trinity_fasta.py "$outdir"/"$stem".longest_isoform.fa "$stem" "$outdir"/"$stem".full_cds.fa
+    echo "Done."
+done