polish: use parallel instead of shell func
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1 changed files with 23 additions and 11 deletions
34
RGBEPP.sh
34
RGBEPP.sh
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@ -46,7 +46,8 @@ while true; do
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*) ARG_F=$2; shift 2 ;;
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esac ;;
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-h|--help)
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echo -e "\t\t\t\t\t\t\tRGB EPP\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
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# echo -e "\t\t\t\t\t\t\t\033[0;31mR\033[0m\033[0;92mG\033[0m\033[0;94mB\033[0m \033[0;33mE\033[0m\033[0;94mP\033[0m\033[0;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
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echo -e "\t\t\t\t\t\t\t\033[0;47;31mR\033[0m\033[0;47;92mG\033[0m\033[0;47;94mB\033[0m\033[0;47m \033[0m\033[0;47;33mE\033[0m\033[0;47;94mP\033[0m\033[0;47;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
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Version: $pkgver\n \
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License: GPL-3.0-only\n \
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Author: Guoyi Zhang\n \
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@ -250,19 +251,30 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
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exit 1
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fi
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current_thread=0
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# current_thread=0
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mkdir -p $DirAlign
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mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT
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cd $DirMerge
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for (( i=0; i<$length_gn; i++ ))
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do
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java -jar $PathMacse -prog alignSequences -seq ${genes[$i]}.fasta -out_AA ../$DirAlign/AA/${genes[$i]}.fasta -out_NT ../$DirAlign/NT/${genes[$i]}.fasta &
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((current_thread++))
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if [ $current_thread -eq $ARG_T ]; then
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wait
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current_thread=0
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fi
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done
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align_by_macse() {
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java -jar $PathMacse -prog alignSequences -seq $1.fasta -out_AA ../$DirAlign/AA/$1.fasta -out_NT ../$DirAlign/NT/$1.fasta &
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}
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export -f align_by_macse
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parallel -j $ARG_T align_by_macse ::: "${genes[@]}"
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# for (( i=0; i<$length_gn; i++ ))
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# do
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# java -jar $PathMacse -prog alignSequences -seq ${genes[$i]}.fasta -out_AA ../$DirAlign/AA/${genes[$i]}.fasta -out_NT ../$DirAlign/NT/${genes[$i]}.fasta &
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# ((current_thread++))
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# if [ $current_thread -eq $ARG_T ]; then
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# wait
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# current_thread=0
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# fi
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# done
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cd -
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fi
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