polish: make genes read by list instead of ls
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parent
7636c65c5a
commit
3a761cbe2a
1 changed files with 28 additions and 8 deletions
36
batch.sh
36
batch.sh
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@ -21,7 +21,7 @@ HELP=false
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### Get some arrays
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ARGS=$(getopt -o c:,f:,h,l:,m:,r:,t: --long contig:,functions:,help,list:,memory:,reference:,threads: -n 'batch.sh' -- "$@")
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ARGS=$(getopt -o c:,f:,g:,h,l:,m:,r:,t: --long contigs:,genes:,functions:,help,list:,memory:,reference:,threads: -n 'batch.sh' -- "$@")
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if [ $? != 0 ]; then
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echo "Failed to parse options." >&2
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exit 1
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@ -30,11 +30,16 @@ eval set -- "$ARGS"
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while true; do
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case "$1" in
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-c|--contig)
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-c|--contigs)
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case "$2" in
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"") ARG_C='scaffolds'; shift 2 ;;
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*) ARG_C=$2; shift 2 ;;
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esac ;;
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-g|--genes)
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case "$2" in
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"") shift 2 ;;
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*) ARG_G=$2; shift 2 ;;
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esac ;;
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-f|--functions)
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case "$2" in
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"") ARG_F='all'; shift 2 ;;
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@ -45,14 +50,15 @@ while true; do
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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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-c\t--contig\tcontings type: scaffolds or contigs\n \
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-c\t--contigs\tcontings type: scaffolds or contigs\n \
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-g\t--genes\tgene file path\n \
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-f\t--functions\tfunctions type (optional): all clean assembly fasta map pre split merge align\n \
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-h\t--help\thelp: show this information\n \
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-l\t--list\tlist file path\n \
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-m\t--memory\tmemory settings (optional, default 16 GB)\n \
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-r\t--reference\treference genome path\n \
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-t\t--threads\tthreads setting (optional, default 8 threads)\n \
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for example: bash $0 -c scaffolds -f all -l list -r Reference.exons.aa.fas \n"
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for example: bash $0 -c scaffolds -f all -l list -g genes -r Reference.exons.aa.fas \n"
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HELP=true
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shift ;;
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-l|--list)
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@ -89,7 +95,9 @@ if [ "$HELP" = false ]; then
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fi
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readarray -t full_names < "$ARG_L"
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readarray -t genes < "$ARG_G"
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length_fn=${#full_names[@]}
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length_gn=${#genes[@]}
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fi
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### Quality control && Trimming
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@ -214,12 +222,18 @@ fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
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## Check if the genes is specified
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if [ -z "$ARG_G" ] ; then
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echo "Argument of genes list missing."
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exit 1
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fi
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mkdir -p $DirMerge
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cd $DirSplit
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for genes in $(ls)
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for (( i=0; i<$length_gn; i++ ))
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do
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cd $genes
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cat * > ../$genes.fasta
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cd ${genes[$i]}
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cat * > ../${genes[$i]}.fasta
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cd ..
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done
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mv *.fasta ../$DirMerge
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@ -229,10 +243,16 @@ fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
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## Check if the genes is specified
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if [ -z "$ARG_G" ] ; then
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echo "Argument of genes list missing."
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exit 1
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fi
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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 genes in $(ls | sed "s@.fasta@@g")
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for (( i=0; i<$length_gn; i++ ))
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do
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java -jar $PathMacse -prog alignSequences -seq ${genes}.fasta -out_AA ../$DirAlign/AA/$genes.fasta -out_NT ../$DirAlign/NT/$genes.fasta
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done
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