calculate_cancer_drug_efficacy

source $vini_dir/globals


vina_version=$1

if [[ -e $WORKDIR/hsa05223_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_exp_named ]] && [[ -e $WORKDIR/hsa05223_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_noexp_named ]]
then
    grep Water $WORKDIR/${CANCER_PATHWAY}_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_${exp}_named > tmp
    SLEMcw=`cat tmp | awk '{print $2}'`
    grep Water $WORKDIR/${CANCER_PATHWAY}_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_${exp}_named > tmp
    SLEMnw=`cat tmp | awk '{print $2}'`
    echo -n "Computing cancer drug effectiveness..."
    > $WORKDIR/tmp
    while read -r line
    do
        echo $line | awk  '{print $1}' > drug    #delete SLEM_ prefix from lines
        sed -i -e 's/SLEM_//g' drug  #delete SLEM_ prefix from lines
        drug=`cat drug`
        if  [ $drug != Water ]                    #avoid the computation for the water
        then
            SLEMcd=`echo $line | awk '{print $2}'`
            grep $drug $WORKDIR/${CANCER_PATHWAY}_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_noexp_named > SLEMn
            SLEMnd=`cat SLEMn | awk '{print $2}'`
            Q1=`echo $ONES / $SLEMcd | bc -l`    #compute (Q1 - Q2) / (Q3 - Q4)
            Q2=`echo $ONES / $SLEMcw | bc -l`    
            Q3=`echo $ONES / $SLEMnd | bc -l`    
            Q4=`echo $ONES / $SLEMnw | bc -l`    
            deltaQ12=`echo $Q1 - $Q2 | bc -l`
            deltaQ34=`echo $Q3 - $Q4 | bc -l`
	    if  [ $deltaQ34 == 0 ]
            then                       #avoid division by zero
                echo "failed to compute efficacy for drug" $drug
            else
                #Qd=`echo $deltaQ12 / $deltaQ34 | bc -l`
                Qd=`echo $SLEMcd / $SLEMnd | bc -l`
                echo $drug $Qd >> $WORKDIR/tmp
            fi
        fi
    done < $WORKDIR/${CANCER_PATHWAY}_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_exp_named
    sort -k2 -n -r $WORKDIR/tmp > $WORKDIR/${CANCER_PATHWAY}_results/${cell_line}_${vina_version}_drug_efficacy
    echo "done." ; echo "Data are in" $WORKDIR/${CANCER_PATHWAY}_results/${cell_line}_${vina_version}_drug_efficacy "file."
else
    echo "If you want to compute the effectiveness of cancer drugs, you need to run the second simulation"
    if  [ -e $WORKDIR/${CANCER_PATHWAY}_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_exp_named ] ; then
        echo "without expression and mutation data."
    else
        echo "with expression and mutation data."
    fi
fi
rm -f $WORKDIR/${CANCER_PATHWAY}_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_${exp}
rm -f $WORKDIR/${CANCER_PATHWAY}_results/SLEM_${vina_version}_values_${cell_line}_thl${therapy_level}_${exp}_reduced
rm -f drug SLEMn tmp