polish: add args, polish all process
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1 changed files with 221 additions and 23 deletions
244
batch.sh
244
batch.sh
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@ -1,44 +1,242 @@
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#!/bin/bash
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### Environment Setting
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pkgver=0.0.1
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DirRaw=00_raw
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DirQcTrim=01_fastp
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DirAssembly=02_spades
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DirFasta=03_contig
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DirMap=04_map
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DirPre=05_pre
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DirSplit=06_split
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DirMerge=07_merge
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DirAlign=08_align
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PathSplitfsata=~/Downloads/PhD/wes/splitfasta-cpp
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PathMacse=/usr/share/java/macse.jar
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PathSortdiamond=/home/guoyi/Downloads/PhD/wes/sortdiamond
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HELP=false
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### Get some arrays
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cd $DirRaw
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ARGS=$(getopt -o c:,f:,h,l:,m:,r:,t: --long contig:,functions:,help,list:,memory:,reference:,threads: -n 'batch.sh' -- "$@")
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if [ $? != 0 ]; then
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echo "Failed to parse options." >&2
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exit 1
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fi
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eval set -- "$ARGS"
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readarray -t full_names < <(ls | awk -F '_' '{print $1 "_" $2 "_" $3 "_" $4}' | uniq)
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readarray -t species_names < <(ls | awk -F '_' '{print $2 "_" $3}' | uniq)
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readarray -t output_names < <(ls | awk -F '_' '{print $2 "_" $3 "_" $4}' | uniq)
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while true; do
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case "$1" in
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-c|--contig)
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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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-f|--functions)
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case "$2" in
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"") ARG_F='all'; shift 2 ;;
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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\tExon 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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-c\t--contig\tcontings type: scaffolds or contigs\n \
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-f\t--functions\tfunctions type (optional): all clean assembly fasta map pre\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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HELP=true
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shift ;;
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-l|--list)
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case "$2" in
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"") shift 2 ;;
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*) ARG_L=$2; shift 2 ;;
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esac ;;
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-m|--memory)
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case "$2" in
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"") ARG_M=16; shift 2 ;;
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*) ARG_M=$2; shift 2 ;;
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esac ;;
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-r|--reference)
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case "$2" in
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"") shift 2 ;;
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*) ARG_R=$2; shift 2 ;;
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esac ;;
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-t|--threads)
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case "$2" in
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"") ARG_T=8; shift 2 ;;
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*) ARG_T=$2; shift 2 ;;
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esac ;;
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--) shift; break ;;
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*) echo "Internal error!"; exit 1 ;;
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esac
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done
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cd ..
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### Get and check some arguments
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length_fn=${#full_names[@]}
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length_sn=${#species_names[@]}
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length_on=${#output_names[@]}
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if [ "$HELP" = false ]; then
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if [ -z "$ARG_L" ]; then
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echo "List argument can't be empty"
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exit 1
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fi
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### Check the arrays
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if [ $length_fn -ne $length_sn ] || [ $length_fn -ne $length_on ] || [ $length_sn -ne $length_on ]
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then
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echo "Please check the amount number of arrays"
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exit 0
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readarray -t full_names < "$ARG_L"
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length_fn=${#full_names[@]}
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fi
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### Quality control && Trimming
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mkdir -p $DirQcTrim
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "clean" ]; then
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for (( i=0; i<$length_fn; i++ )); do
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fastp -i $DirRaw/${full_names[$i]}_R1.fastq.gz -I $DirRaw/${full_names[$i]}_R2.fastq.gz -j ${species_names[$i]}.json -h ${species_names[$i]}.html -o $DirQcTrim/${output_names[$i]}_R1.fastq.gz -O $DirQcTrim/${output_names[$i]}_R2.fastq.gz -w 4
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done
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## Prepare
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mkdir -p $DirQcTrim
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## Quality control and trimming using fastp
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for (( i=0; i<$length_fn; i++ )); do
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fastp -i $DirRaw/${full_names[$i]}_R1.fastq.gz -I $DirRaw/${full_names[$i]}_R2.fastq.gz -j $DirQcTrim/${full_names[$i]}.json -h $DirQcTrim/${full_names[$i]}.html -o $DirQcTrim/${full_names[$i]}_R1.fastq.gz -O $DirQcTrim/${full_names[$i]}_R2.fastq.gz -w $ARG_T
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done
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fi
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### De novo assembly
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mkdir -p $DirAssembly
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "assembly" ]; then
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## Prepare
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mkdir -p $DirAssembly
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## De novo assembly using spades
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for (( i=0; i<$length_fn; i++ )); do
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mkdir -p $DirAssembly/${full_names[$i]}
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spades.py --pe1-1 $DirQcTrim/${full_names[$i]}_R1.fastq.gz --pe1-2 $DirQcTrim/${full_names[$i]}_R2.fastq.gz -t $ARG_T -m $ARG_M --careful --phred-offset 33 -o $DirAssembly/${full_names[$i]}
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# -k 96,107,117,127 \
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done
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fi
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### Moving scaffords or Contigs out
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "fasta" ]; then
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## Check if the contigs type is specified
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if [ -z "$ARG_C" ] ; then
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echo "Argument of contig type missing."
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exit 1
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fi
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## Prepare
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mkdir -p $DirFasta
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## Move the assemblied fasta file to the folder
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if [ "$ARG_C" = "scaffolds" ] || [ "$ARG_C" = "contigs" ] ; then
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for (( i=0; i<$length_fn; i++ )); do
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cp $DirAssembly/${full_names[$i]}/$ARG_C.fasta $DirFasta/$ARG_C/${full_names[$i]}.fasta
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done
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fi
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fi
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### Mapping
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "map" ]; then
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## Check if the reference or contigs type is specified
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if [ -z "$ARG_R" ] || [ -z "$ARG_C" ] ; then
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echo "Argument of reference or contig type missing."
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exit 1
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fi
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## Prepare
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mkdir -p $DirMap
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## Index reference database
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cd $DirFasta/$ARG_C
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diamond makedb --db Reference --in $ARG_R
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cd -
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## Blastx for mapping DNA sequences to protein reference sequence
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cd $DirFasta/$ARG_C
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for (( i=0; i<$length_fn; i++ )); do
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diamond blastx -d Reference.dmnd -q ${full_names[$i]}.fasta -o ${full_names[$i]}.m8 \
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--outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen gaps ppos qframe qseq
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# subject: reference; query: align-aimed
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#1: qseqid: Query Seq-id
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#2: sseqid: Subject Seq - id
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#3: pident: Percentage of identical matches
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#4: length: Alignment length
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#5: mismatch: Number of mismatches
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#6: gapopen: Number of gap openings
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#7: qstart: Start of alignment in query
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#8: qend: End of alignment in query
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#9: sstart: Start of alignment in subject
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#10: send: End of alignment in subject
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#11: evalue: Expect value
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#12: bitscore: Bit score
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#13: qlen: Query sequence length 比对序列长度
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#14: slen: Subject sequence length
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#15: gaps: Total number of gaps
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#16: ppos: Percentage of positive - scoring matches
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#17: qframe: Query frame (frames in ECPP.sh)
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#18: qseq: Aligned part of query sequence
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done
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cd -
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mv $DirFasta/$ARG_C/*.m8 $DirMap
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "pre" ]; then
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mkdir -p $DirPre
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for (( i=0; i<$length_fn; i++ )); do
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$PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta
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done
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "split" ]; then
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mkdir -p $DirSplit
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cd $DirPre
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for (( i=0; i<$length_fn; i++ )); do
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$PathSplitfsata ${full_names[$i]}.fasta
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done
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find . -mindepth 1 -maxdepth 1 -type d -exec mv {} ../$DirSplit \;
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cd -
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
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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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do
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cd $genes
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cat * > ../$genes.fasta
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cd ..
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done
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mv *.fasta ../$DirMerge
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cd -
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
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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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do
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java -jar $PathMacse -prog alignSequences -seq ${genes}.fasta -out_AA ../$DirAlign/AA/$genes.fasta -out_NT ../$DirAlign/NT/$genes.fasta
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done
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cd -
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fi
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for (( i=0; i<$length_fn; i++ )); do
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mkdir -p $DirAssembly/${species_names[$i]}
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spades.py --pe1-1 $DirQcTrim/${output_names[$i]}_R1.fastq.gz --pe1-2 $DirQcTrim/${output_names[$i]}_R2.fastq.gz -t 8 -k 97,107,117,127 -m 14 --careful --phred-offset 33 -o $DirAssembly/${species_names[$i]}
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done
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