20261002

99.scripts_v2/02.orthofinder.sh

@@ -1,3 +1,7 @@
+#!/bin/bash
+
+set -euo pipefail
+
 # prepare input files for orthofinder
 mkdir input_pep
 cp ../11.reference_v2/pep/primary_transcripts/*.pep.fa input_pep
@@ -17,5 +21,18 @@ done
 pueue add -- orthofinder -t 12 -a 4 -f input_pep/core -o orthofinder_out
 
 # assign outgroups
-pueue add -- orthofinder -t 12 -a 4 --assign input_pep/outgroup --core orthofinder_out/Results_Hippophae_only
+pueue add -- orthofinder -t 12 -a 4 --assign input_pep/outgroup --core orthofinder_out/Results_Aug03
 
+ln -s orthofinder_out/Results_Aug03 Hippophae_only
+ln -s orthofinder_out/Results_Aug03_1/ Hippophae_outgroup
+
+# get all cds into a file
+echo -ne >all_cds.fa
+for i in ../11.reference_v2/cds/*.cds.fa; do
+    base=$(basename "$i" .cds.fa)
+    echo "Processing $base"
+    sed "s/>/>${base}@/g" "$i" >>all_cds.fa
+done
+
+# get og list and extract cds sequences for each og
+pueue add -- python3 "$PROJECTHOME"/99.scripts_v2/utils/get_og_seqs.py -d Hippophae_outgroup/Single_Copy_Orthologue_Sequences -a all_cds.fa -o ogs_cds