2026-08-02

2026-08-02 14:18:07 +08:00
parent 7f4e888e6a
commit e398109a10
14 changed files with 14496 additions and 7653 deletions
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+set -euo pipefail
+
+cd "$PROJECTHOME"/11.reference_v2
+
+# HG sequences name should be changed.
+cd raw
+seqkit replace -k HG.map.txt -p "^(\S+).*$" -r "{kv}" GCA_030763125.1_ASM3076312v1_genomic.fna -o HG.fa -K --f-use-regexp
+
+# MG & ZG use hapA genome
+grep -Fwf MG.target.txt MG.gff > MG.target.gff
+grep -Fwf ZG.target.txt ZG.gff > ZG.target.gff
+
+# Extract CDS sequences from GFF3 files using gffread
+pueue add -- gffread -g raw/HN.fa -x HN.cds.fa -y HN.pep.fa raw/HN.gff3
+pueue add -- gffread -g raw/HG.fa -x HG.cds.fa -y HG.pep.fa raw/Hippophae_gyantsensis.gff
+pueue add -- gffread -g raw/HS.fa -x HS.cds.fa -y HS.pep.fa raw/HS.gff3
+pueue add -- gffread -g raw/YN.genome.fa -x YN.cds.fa -y YN.pep.fa raw/YN.gff3
+pueue add -- gffread -g raw/ZG.genome.fa -x ZG.cds.fa -y ZG.pep.fa raw/ZG.target.gff
+pueue add -- gffread -g raw/ZJ.genome.fa -x ZJ.cds.fa -y ZJ.pep.fa raw/ZJ.gff
+pueue add -- gffread -g raw/ZY.fa -x ZY.cds.fa -y ZY.pep.fa raw/ZY.gff3
+pueue add -- gffread -g raw/Hippophae_tibetana.genomic.fasta -x HT.cds.fa -y HT.pep.fa raw/Hippophae_tibetana.mRNA.gff
+pueue add -- gffread -g raw/MG.genome.fasta -x MG.cds.fa -y MG.pep.fa raw/MG.target.gff
+cp raw/EA.gff3.cds EA.cds.fa
+cp raw/EM.genome.cds.fasta EM.cds.fa
+cp raw/EA.gff3.pep EA.pep.fa
+cp raw/EM.pep.fasta EM.pep.fa
+
+mkdir pep
+mkdir cds
+mv ./*.cds.fa cds
+mv ./*.pep.fa pep
+
+cd pep
+primary_transcript ./ last_dot
+
+# EM基因命名特殊性，导致直接使用primary_transcript会出现问题，直接复制即可
+cp EM.pep.fa primary_transcripts/EM.pep.fa
+
@@ -0,0 +1,21 @@
+# 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_Hippophae_only
+