#!/bin/bash

set -euo pipefail

# prepare input files for orthofinder
mkdir input_pep
cp ../11.reference_v2/pep/primary_transcripts/*.pep.fa input_pep
mkdir input_pep/core
mkdir input_pep/outgroup
mv input_pep/EA.pep.fa input_pep/outgroup
mv input_pep/EM.pep.fa input_pep/outgroup
mv input_pep/ZJ.pep.fa input_pep/outgroup
mv input_pep/*.pep.fa input_pep/core
for i in input_pep/*/*.pep.fa; do
    base=$(basename "$i" .pep.fa)
    echo "Processing $base"
    sed -i "s/>/>${base}@/g" "$i"
done

# run orthofinder with Hippophae genomes as backbone
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_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