Remove scripts for HipSTR STRetch STRscan LobSTR

getFMR1result.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## pipeline.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : script to get automatically results from pipeline.sh script in a tsv format on the FMR1 X fragile locus
-## Usage : 
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191215
-## last revision date : 20191215
-## Known bugs : None
-
-cd /work/gad/shared/analyse/STR/pipeline/
-(
-    echo -e 'dijenxxx\tEH\tTred\tGangSTR'
-    ls -d dijen* | while read dijen
-    do
-        (
-            echo "$dijen"
-            awk '$1 == "chrX" && $2 == "146993568" {print $5}' $dijen/eh/$dijen.vcf |
-                sed 's@<STR\([0-9]\+\)>@\1@g'
-            gunzip -c $dijen/tredparse/$dijen.tred.vcf.gz |
-                awk '$1 == "chrX" && $2 == "146993569" && $3 == "FXS" {print $8}' |
-                tr ';' '\n' |
-                awk -F '=' '$1 == "RPA" {print $2}'
-            awk '$1 == "chrX" && $2 == "146993569" {print $9 " " $10}' $dijen/gangstr/$dijen.vcf |
-                python3 -c 'import sys; format, genotype = sys.stdin.read().split(); print(genotype.split(":")[format.split(":").index("REPCN")]) if genotype != "." else print(".")'
-        ) |
-            tr '\n' '\t'
-        echo
-    done
-) > results
-
-

launch_hipstr.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## launch_wrapper_hipstr.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : script to launch the wrapper for qsubing HipSTR script for STR detection
-## Usage : FIXME
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191104
-## last revision date : 20191104
-## Known bugs : None
-
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/HipSTR/$DATE"
-OUTPUTPREFIX="$OUTPUTDIR/$(basename -s .bam "$INPUTFILE")_$DATE"
-OUTPUTFILE="$OUTPUTPREFIX.vcf.gz"
-LOGFILE="$OUTPUTDIR/$DATE.log"
-
-# Launch the script on local host with --local option and on SGE with qsub without the --local option
-if [ $# -eq 1 ] && [ "x$1" = x--local ]
-then
-    mkdir -p "$OUTPUTDIR"
-    INPUTFILE="$INPUTFILE" OUTPUTFILE="$OUTPUTFILE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_hipstr.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 2 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTFILE="$OUTPUTFILE",LOGFILE="$LOGFILE" wrapper_hipstr.sh
-fi

launch_lobstr.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## launch_wrapper_lobstr.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : script to launch the wrapper for qsubing LobSTR script for STR detection
-## Usage : FIXME
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191104
-## last revision date : 20191104
-## Known bugs : None
-
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18/dijen017.sorted.bam
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/LobSTR/$DATE"
-OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
-LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
-
-# Launch the script on local host with --local option and on SGE with qsub without the --local option
-if [ $# -eq 1 ] && [ "x$1" = x--local ]
-then
-    mkdir -p "$OUTPUTDIR"
-    INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_lobstr.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_lobstr.sh
-fi

launch_stretch.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## launch_wrapper_stretch.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : script to launch the wrapper for qsubing STRetch script for STR detection
-## Usage : FIXME
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191118
-## last revision date : 20191127
-## Known bugs : None
-
-# INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
-
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/shortdijen017/dijen017.short.bam
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/STRetch/$DATE"
-LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
-
-# Launch the script on local host with --local option and on SGE with qsub without the --local option
-if [ $# -eq 1 ] && [ "x$1" = x--local ]
-then
-    mkdir -p "$OUTPUTDIR"
-    INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_stretch.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 16 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_stretch.sh
-fi

wrapper_hipstr.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## wrapper_hipstr.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : a wrapper for qsubing HipSTR script for STR detection
-## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_hipstr.sh
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191104
-## last revision date : 20191104
-## Known bugs : None
-
-
-# Log file path option
-if [ -z "$LOGFILE" ]
-then
-    LOGFILE=hipstr.$(date +"%F_%H-%M-%S").log
-fi
-
-# Logging
-exec 1>> "$LOGFILE" 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-
-# Check if input file exists
-if [ ! -f "$INPUTFILE" ]
-then
-    echo "Input file '$INPUTFILE' does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-# Check if output prefix is specified
-if [ -z "$OUTPUTFILE" ]
-then
-    echo "Output file is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-# Launch script command and check exit code
-echo "command : FIXME"
-
-/work/gad/shared/bin/hipstr/HipSTR-2019-11-04/HipSTR \
-    --bams "$INPUTFILE" \
-    --fasta /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
-    --str-vcf "$OUTPUTFILE"
-
-#    --regions /work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed
-
-hipstr_exitcode=$?
-
-echo "hipstr exit code : $hipstr_exitcode"
-if [ $hipstr_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-echo "$(date +"%F_%H-%M-%S"): END"

wrapper_lobstr.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## wrapper_lobstr.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : a wrapper for qsubing LobSTR script for STR detection
-## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_lobstr.sh
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191104
-## last revision date : 20191104
-## Known bugs : None
-
-
-# Log file path option
-if [ -z "$LOGFILE" ]
-then
-    LOGFILE=lobstr.$(date +"%F_%H-%M-%S").log
-fi
-
-# Logging
-exec 1>> "$LOGFILE" 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-
-# Check if input file exists
-if [ ! -f "$INPUTFILE" ]
-then
-    echo "Input file '$INPUTFILE' does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-# Check if output prefix is specified
-if [ -z "$OUTPUTPREFIX" ]
-then
-    echo "Output prefix is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-# Launch script command and check exit code
-echo "command : FIXME"
-#FIXME
-echo "command : FIXME /work/gad/shared/bin/lobstr/lobSTR-4.0.6/bin/lobSTR \
-    --bampair -f /archive/gad/shared/bam_new_genome_temp/dijen017.bam \
-    --rg-lib /archive/gad/shared/bam_new_genome_temp/dijen017.bam \
-    --rg-sample /archive/gad/shared/bam_new_genome_temp/dijen017.bam \
-    --index-prefix /work/gad/shared/bin/lobstr/ref/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ \
-    -o ~/test \
-    -v"
-
-/work/gad/shared/bin/lobstr/lobSTR-4.0.6/bin/lobSTR \
-    --bampair -f "$INPUTFILE" \
-    --rg-lib "$INPUTFILE" \
-    --rg-sample "$INPUTFILE" \
-    --index-prefix /work/gad/shared/bin/lobstr/ref/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ \
-    -o "$OUTPUTPREFIX" \
-    -v 
-
-
-lobstr_exitcode=$?
-
-echo "lobstr exit code : $lobstr_exitcode"
-if [ $lobstr_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-echo "$(date +"%F_%H-%M-%S"): END"

wrapper_samtoolssortbyread.sh

-#! /bin/sh
-
-samtools sort -n -@64 --check=quiet -T sortbyread  /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-26  -o /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-26/dijen017.sorted.bam /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/dijen017.bam

wrapper_stretch.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## Version: 0.0.1
-## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
-## Description: a wrapper for qsubing STRetch script for STR detection
-## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_stretch.sh
-
-
-# Log file path option
-if [ -z "$LOGFILE" ]
-then
-    LOGFILE=stretch.$(date +"%F_%H-%M-%S").log
-fi
-
-# Logging
-exec 1>> "$LOGFILE" 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-
-# Check if input file exists
-if [ ! -f "$INPUTFILE" ]
-then
-    echo "Input file '$INPUTFILE' does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-# Check if output prefix is specified
-if [ -z "$OUTPUTPREFIX" ]
-then
-    echo "Output prefix is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-# Launch script command and check exit code
-echo "cd "$OUTPUTDIR"
-/work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \
-    run -p input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
-    /work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \
-    "$INPUTFILE""
-
-cd "$OUTPUTDIR"
-/work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \
-    run -p input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
-    /work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \
-    "$INPUTFILE"
-
-stretch_exitcode=$?
-
-echo "stretch exit code : $stretch_exitcode"
-if [ $stretch_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-echo "$(date +"%F_%H-%M-%S"): END"

wrapper_strscan.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## wrapper_gangstr.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : a wrapper for qsubing STRScan script for STR detection
-## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_strscan.sh
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191115
-## last revision date : 20191115
-## Known bugs : None
-
-
-# Log file path option
-if [ -z "$LOGFILE" ]
-then
-    LOGFILE=strscan.$(date +"%F_%H-%M-%S").log
-fi
-
-# Logging
-exec 1>> "$LOGFILE" 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-
-# Check if input file exists
-if [ ! -f "$INPUTFILE" ]
-then
-    echo "Input file '$INPUTFILE' does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-# Check if output prefix is specified
-if [ -z "$OUTPUTPREFIX" ]
-then
-    echo "Output prefix is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-# Launch script command and check exit code
-echo "command : /work/gad/shared/bin/strscan/STRScan_2019-11-05/STRScan \
-    -i "$INPUTFILE" \
-    -p /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
-    -o "$OUTPUTFILE""
-
-/work/gad/shared/bin/strscan/STRScan_2019-11-05/STRScan \
-    -i "$INPUTFILE" \
-    -p /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
-    -o "$OUTPUTFILE"
-
-strscan_exitcode=$?
-
-echo "strscan exit code : $strscan_exitcode"
-if [ $strscan_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-echo "$(date +"%F_%H-%M-%S"): END"