Mercurial > repos > charles-bernard > alfa
diff ALFA/alfa_wrapper.sh @ 18:a1e2ab10b317 draft
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| author | charles-bernard |
|---|---|
| date | Tue, 11 Oct 2016 09:18:48 -0400 |
| parents | |
| children | 1239f24962d8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ALFA/alfa_wrapper.sh Tue Oct 11 09:18:48 2016 -0400 @@ -0,0 +1,233 @@ +#!usr/bin/bash + +######################################################################################################### +# ARGUMENTS FROM alfa_wrapper.xml # +######################################################################################################### +configFile=$1; +logReport=$2; +sed -i -e '/^$/d; s/\t//g;' $configFile; +printf "__________________________________________________________________\n\n" > $logReport +printf " ALFA CONFIG \n" >> $logReport +printf "__________________________________________________________________\n" >> $logReport +cat $configFile >> $logReport + +######################################################################################################### +# INITIALIZATION OF THE VARIABLES from $configFile # +######################################################################################################### +#_INPUT1 +annotationSource=`grep -P '^annotationSource ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +if [ "$annotationSource" == "personal_gtf" ]; then + annotationFile=`grep -P '^annotationFile ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +elif [ "$annotationSource" == "built_in_index" ]; then + built_in_index_prefix=`grep -P '^built_in_index_prefix ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +else + strandedIndex=`grep -P '^strandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + unstrandedIndex=`grep -P '^unstrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +fi + +#_INPUT2 +readsType=`grep -P '^readsType ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +readsFileList=`grep -P '^readsFile\[[0-9]+\] ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +readsLabelList=`grep -P '^readsLabel\[[0-9]+\] ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + +#_OUTPUT CHOICES +plotChoice=`grep -P '^plotChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +countFileChoice=`grep -P '^countFileChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +indexChoice=`grep -P '^indexChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + +#_OUTPUT OPTIONS +strandness=`grep -P '^strandness ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +categoriesDepth=`grep -P '^categoriesDepth ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +plotFormat=`grep -P '^plotFormat ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +plotThresholdChoice=`grep -P '^plotThresholdChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +if [ "$plotThresholdChoice" == "True" ]; then + yMin=`grep -P '^yMin ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + yMax=`grep -P '^yMax ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +fi + +#_OUTPUT FILES +if [ "$plotChoice" == "True" ]; then + if [ "$plotFormat" == "pdf" ]; then + outputPdf=`grep -P '^outputPdf ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + elif [ "$plotFormat" == "svg" ]; then + outputCategoriesSvg=`grep -P '^outputCategoriesSvg ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + outputBiotypesSvg=`grep -P '^outputBiotypesSvg ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + else + outputCategoriesPng=`grep -P '^outputCategoriesPng ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + outputBiotypesPng=`grep -P '^outputBiotypesPng ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + fi +fi +if [ "$countFileChoice" == "True" ]; then + outputCountFile=`grep -P '^outputCountFile ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +fi +if [ "$indexChoice" == "True" ]; then + outputStrandedIndex=`grep -P '^outputStrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; + outputUnstrandedIndex=`grep -P '^outputUnstrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; +fi + +######################################################################################################### +# CREATION OF A TMP DIRECTORY FOR THE OUTPUT FILES OF ALFA AND cd # +######################################################################################################### +outputDirectory=`mktemp -d /export/home1/users/biocomp/chbernar/galaxy/database/tmp/tmpXXXXXX`; +if [ -d $outputDirectory ]; then + chmod -R ugo+wrx $outputDirectory; + rm -R $outputDirectory; +fi +mkdir $outputDirectory; +chmod -R ugo+wrx $outputDirectory; +cd $outputDirectory; + +######################################################################################################### +# TEST OF INPUT1 # +######################################################################################################### +if [ "$annotationSource" == "index" ]; then + #need to copy the files.dat to .*index because ALFA requires the extension ".(un)stranded.index" + index="index" + cp $strandedIndex $index".stranded.index" + cp $unstrandedIndex $index".unstranded.index" +fi + +######################################################################################################### +# TEST OF INPUT2 AND DETERMINATION OF PYTHON READS INPUT ARGUMENT # +######################################################################################################### +readsListLen=`echo "$readsFileList" | wc -l`; +readsInput=""; +for (( i = 1; i <= readsListLen; i++ )) do + readsFile[$i]=`echo "$readsFileList" | awk -v i=$i 'NR==i'`; + readsLabel[$i]=`echo "$readsLabelList" | awk -v i=$i 'NR==i' | sed -e 's/ /_/g'`; + if [ "$readsType" == "bam" ]; then + bamSorted=`samtools view -H "${readsFile[$i]}" | grep -c 'SO:unsorted'` + if [ "$bamSorted" != "0" ] ; then + samtools sort ${readsFile[$i]} ${readsFile[$i]} + fi + else + #need to copy the file.dat to tmp.bedgraph because ALFA requires the extension ".bedgraph" + bedgraphFile="tmpBedgraph_"$i + cp ${readsFile[$i]} $bedgraphFile".bedgraph" + readsFile[$i]=$bedgraphFile + fi + if [ "${readsLabel[$i]}" == "" ]; then + readsLabel[$i]="sample_""$i"; + fi + readsInput=$readsInput" "${readsFile[$i]}" "${readsLabel[$i]}; +done + +######################################################################################################### +# DETERMINATION OF THE APPROPRIATE SCRIPTS ARGUMENTS # +######################################################################################################### +scriptPath="/export/home1/users/biocomp/chbernar/galaxy/tools/alfa/"; +if [ "$annotationSource" == "index" ]; then + scriptInput="-g $index -i ""$readsInput"; +elif [ "$annotationSource" == "built_in_index" ]; then + scriptInput="-g $built_in_index_prefix -i ""$readsInput"; +else + scriptInput="-a $annotationFile -i ""$readsInput"; +fi +if [ "$readsType" = "bedgraph" ]; then + scriptInput=$scriptInput" --bedgraph"; +fi +scriptStrandness="-s "$strandness +scriptCategoriesDepth="-d "$categoriesDepth +if [ "$plotChoice" == "True" ]; then + if [ "$plotFormat" == "pdf" ]; then + scriptPlotOutput="--pdf plotFile.pdf"; + else + scriptPlotOutput="--"$plotFormat" plotFile"; + fi + if [ "$plotThresholdChoice" == "True" ]; then + scriptPlotOutput=$scriptPlotOutput" -t ""$yMin"" ""$yMax" + fi +else + scriptPlotOutput="--n"; +fi + +######################################################################################################### +# DISPLAY ALFA PROCESS # +######################################################################################################### +printf "__________________________________________________________________\n\n" >> $logReport +printf " ALFA PROCESS \n" >> $logReport +printf "__________________________________________________________________\n" >> $logReport + +if [ "$plotChoice" == "False" ] && [ "$countFileChoice" == "False" ] && [ "$indexChoice" == "False" ]; then +cat <<error 1>&2 + +No output to return. +Process Aborted +error +exit 0 +fi + +printf "Command:\n" >> $logReport +echo "python ""$scriptPath"ALFA.py $scriptInput $scriptStrandness $scriptCategoriesDepth $scriptPlotOutput >> $logReport; +printf "\n******************************************************************\n" >> $logReport +printf "Temporary Output Directory:\n" >> $logReport +echo $outputDirectory >> $logReport +printf "\n******************************************************************\n" >> $logReport +printf "ALFA prompt:\n" >> $logReport +python "$scriptPath"ALFA.py $scriptInput $scriptStrandness $scriptCategoriesDepth $scriptPlotOutput >> $logReport 2>errorFile; +printf "\n******************************************************************\n" >> $logReport + +######################################################################################################### +# REDIRECTION OF ERRORS - TMP SOURCE ALFA.PY MUST BE CORRECTED SOON # +######################################################################################################### +if [[ -s errorFile ]]; then + #When the option --n is enabled, alfa prints '### End of the program' in stderr even if the process worked- + #The following lines to avoid the tool from crashing in this case + endProgram=`grep -c '### End of program' errorFile` + if [ "$endProgram" == "0" ]; then + #When alfa prints '### End of program' in stdout, all the messages in stderr are considered + #as warnings and not as errors. True errors make the script exits with code "2" + endProgram=`grep -c '### End of program' $logReport` + if [ "$endProgram" == "0" ]; then + >&2 printf "The script ALFA.py encountered the following error:\n\n" + >&2 cat errorFile + printf "ALFA error:\n" >> $logReport + cat errorFile >> $logReport + printf "\n******************************************************************\n" >> $logReport + exit 2 + else + >&2 printf "The script ALFA.py encountered the following warning:\n\n" + >&2 cat errorFile + printf "ALFA warning:\n" >> $logReport + cat errorFile >> $logReport + printf "\n******************************************************************\n" >> $logReport + fi + fi +fi + +######################################################################################################### +# OUTPUT REDIRECTIONS # +######################################################################################################### +if [ "$plotChoice" == "True" ]; then + if [ "$plotFormat" == "pdf" ]; then + mv "plotFile.pdf" $outputPdf; + elif [ "$plotFormat" == "png" ]; then + mv "plotFile.categories.png" $outputCategoriesPng; + mv "plotFile.biotypes.png" $outputBiotypesPng; + else + mv "plotFile.categories.svg" $outputCategoriesSvg; + mv "plotFile.biotypes.svg" $outputBiotypesSvg; + fi +fi +if [ "$countFileChoice" == "True" ]; then + > countFile; + for (( i = 1; i <= readsListLen; i++ )) do + printf "##LABEL: "${readsLabel[$i]}"\n\n" >> countFile; + cat ${readsLabel[$i]}".categories_counts" >> countFile; + printf "__________________________________________________________________\n" >> countFile; + done + mv countFile $outputCountFile; +fi +if [ "$indexChoice" == "True" ]; then + if [ "$annotationSource" == "index" ]; then + mv $strandedIndex $outputStrandedIndex + mv $unstrandedIndex $outputUnstrandedIndex + elif [ "$annotationSource" == "built_in_index" ]; then + cp $built_in_index_prefix".stranded.index" $outputStrandedIndex + cp $built_in_index_prefix".unstranded.index" $outputUnstrandedIndex + else + annotationFileName=`grep -P -o '[^/]*\.dat$' <<< $annotationFile` + mv $annotationFileName".stranded.index" $outputStrandedIndex + mv $annotationFileName".unstranded.index" $outputUnstrandedIndex + fi +fi \ No newline at end of file