genome_prepare/script/blast_uniprot.sh

#!/bin/bash
#set -e
type="proteins"
script_path=$(dirname `realpath $0`)
outdir="."
declare -A software 
software["CDS"]="diamond blastx"
software["proteins"]="diamond blastp"


usage(){
    echo -e "Usage:"
    echo -e "\t$0 -i cds.fa -o outdir -t CDS -d uniprot.fa  -g uniprot.go.tsv"
    echo -e "OPTIONS:"
	echo -e "\t-h: help information"
    echo -e "\t-i: fasta file"
    echo -e "\t-o: output dir"
    echo -e "\t-t: proteins or CDS default:proteins"
    echo -e "\t-d: uniprot species fasta"
    echo -e "\t-g: uniprot species go annotation"
    exit 1
}

while getopts 'd:g:t:i:o:h' OPT;do
    case $OPT in
        h) usage;;
        d) uniprot_fasta="$OPTARG";;
		t) type="$OPTARG";;
        i) fasta="$OPTARG";;
        o) outdir="$OPTARG";;
        g) uniprot_go="$OPTARG";;
        ?) usage;;
    esac
done

if [[ ! $uniprot_fasta ]] || [[ ! -s $fasta ]] || [[ ! $uniprot_go ]] 
then
	usage
fi

if [[ ! ${software[${type}]} ]]
then
    echo "ERROR:unknown -t $type" 
    usage
fi

mkdir -p $outdir
diamond makedb --in $uniprot_fasta -d $uniprot_fasta
${software[${type}]}  -q $fasta -d ${uniprot_fasta}.dmnd -o $outdir/blast.up.txt  -e 0.00001 -f 6 -p 12 --more-sensitive --max-target-seqs 5
cut -f 1,2 -d "|" $outdir/blast.up.txt|sed 's/\t.*|/\t/'|awk -F"\t" '!a[$1]++{print}'  > $outdir/gid_upid
awk 'BEGIN{FS=OFS="\t"}FNR==NR{a[$1]=$3}FNR!=NR{if(a[$2]){GO=a[$2]}else{GO="-"};print $1,GO}' $uniprot_go $outdir/gid_upid > $outdir/uniprot.go