Remove unused scripts and replace triplets by str

README.md

@@ -18,11 +18,11 @@
    - `wrapper_transfer.sh`
    - `wrapper_tredparse.sh`
 4. Launch `getResults.py`. Warning, don't overwrite existing files.
-5. Specify input directory in `triplets_plotly.py` and in `launch_triplets_plotly.sh`.
-6. Launch `launch_triplets_plotly.sh`.
-7. Specify input directory in `triplets_outliers.py` and in `launch_triplets_outliers.sh`.
-8. Change z-score threshold if necessary in `triplets_outliers.py`.
-9. Launch `launch_triplets_outliers.sh`. Dependency: `patho.csv`.
+5. Specify input directory in `str_plotly.py` and in `launch_str_plotly.sh`.
+6. Launch `launch_str_plotly.sh`.
+7. Specify input directory in `str_outliers.py` and in `launch_str_outliers.sh`.
+8. Change z-score threshold if necessary in `str_outliers.py`.
+9. Launch `launch_str_outliers.sh`. Dependency: `patho.csv`.
 10. Get files (i.e.: `scp 'an1770de@ssh-ccub.u-bourgogne.fr:/work/gad/shared/analyse/STR/results/*' .`)
 
 

fake_pipeline.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## launch_pipeline.sh
-## Version : 0.0.1
-## Licence : aGPLv3
-## Description: used to test if pipeline is parallelized on n machines
-## Usage: Launched in place of pipeline.sh. To use it, replace pipeline.sh by fake_pipeline.sh in launch_pipeline.sh
-## Output: FIXME
-## Requirements: FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191208
-## last revision date : 20200215
-## Known bugs : None
-
-SAMPLE="$1"
-
-# Check if sample is specified
-if [ -z "$SAMPLE" ]
-then
-    echo "Sample is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    exit 1
-fi
-
-DURATION=$((RANDOM%15+5))
-
-echo "Starting $SAMPLE"
-
-sleep $DURATION
-
-echo "    Finished $SAMPLE ($DURATION sec)"

launch_ehdn_profile.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## Version: 0.0.1
-## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
-## Description: script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
-
-
-INPUTFILE=/work/gad/shared/analyse/STR/pipeline/dijen073/dijen073.bam
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunterDeNovo/$DATE"
-OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
-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="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_profile.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_ehdn_profile.sh
-fi

launch_expansionhunter.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## Version: 0.0.1
-## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
-## Description: script to launch the wrapper for qsubing ExpansionHunter script for STR detection
-
-
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen561.bam
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunter/$DATE"
-OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
-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="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
-fi

launch_gangstr.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## Version: 0.0.1
-## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
-## Description: script to launch the wrapper for qsubing GangSTR script for STR detection
-
-
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/GangSTR/$DATE"
-OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
-LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
-INSERTMEAN="359.4"
-INSERTDEV="80.1204"
-
-# 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="$LOGFILE" INSERTMEAN="$INSERTMEAN" INSERTDEV="$INSERTDEV" "$(dirname "$0")/wrapper_gangstr.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE",INSERTMEAN="$INSERTMEAN",INSERTDEV="$INSERTDEV" wrapper_gangstr.sh
-fi

launch_triplets_outliers.py → launch_str_outliers.py

 #! /bin/sh
 
-SCRIPT="$(dirname "$(readlink -f "$0")")/triplets_outliers.py"
+SCRIPT="$(dirname "$(readlink -f "$0")")/str_outliers.py"
 
 cd '/work/gad/shared/analyse/STR/results' || exit 1
 for locus_tsv in $(ls *.tsv | grep -v outliers); do

launch_triplets_plotly.sh → launch_str_plotly.sh

 #! /bin/sh
 
-SCRIPT="$(dirname "$(readlink -f "$0")")/triplets_plotly.py"
+SCRIPT="$(dirname "$(readlink -f "$0")")/str_plotly.py"
 
 cd '/work/gad/shared/analyse/STR/results' || exit 1
 for locus_tsv in *.tsv; do

launch_transfer.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## Version: 0.0.1
-## Licence: AGPLv3
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Description: script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
-
-
-INPUTFILE="/archive/gad/shared/bam_new_genome_temp/dijen016.bam"
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/Data"
-LOGFILE="$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="$INPUTFILE" OUTPUTDIR="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_transfer.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_transfer.sh
-fi

launch_tredparse.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## Version: 0.0.1
-## Licence: AGPLv3
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Description: script to launch the wrapper for qsubing Tredparse script for STR detection
-
-
-
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen561.bam
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/Tredparse/$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="$INPUTFILE" OUTPUTDIR="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_tredparse.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_tredparse.sh
-fi

triplets_outliers.py → str_outliers.py

 #! /usr/bin/env python3
 
 ### ASDP PIPELINE ###
-## triplets_outliers.py
 ## Version : 0.0.1
 ## Licence : FIXME
 ## Description : script to get automatically outliers from expansion pipeline results from getResults.py

triplets_plotly.py → str_plotly.py

 #! /usr/bin/env python3
 
 ### ASDP PIPELINE ###
-## triplets_plotly.py
 ## Version : 0.0.1
 ## Licence : FIXME
 ## Description : script to get automatically graphics from expansion pipeline results from getResults.py with Plotly