add_expressions_to_receptors

NULL=0
ONES=1
seven=7

cosmic=`cat $WORKDIR/cosmic`
> $WORKDIR/receptors_contracted.tmp

while read -r line #add z_score and normalized gene exp factor to receptors_contracted file (5th and 6th column)
do
    flag=`echo $line | awk '{print $4}'`
    Uniprot_ID=`echo $line | awk '{print $3}'` #check if entry is protein or compound
    nochars=`echo -n $Uniprot_ID | wc -c`

    if  [ $nochars -gt $seven ]
    then
        entry=`echo $Uniprot_ID | head -c 7`
    else
        entry=protein
    fi

    if  [ $entry != pubchem ]
    then                                                                #we have a protein
        > $WORKDIR/tmp
        grep $Uniprot_ID ./genes/expression_scores.csv > $WORKDIR/tmp
        lines=`wc -l < $WORKDIR/tmp`
        if  [[ $lines -eq $NULL ]] || [[ $flag == "F" ]] 
        then
            z_score=0.000
        else
            if  [ $lines -ne $ONES ]
            then
                head -1 $WORKDIR/tmp > $WORKDIR/tmp2 ; mv $WORKDIR/tmp2 $WORKDIR/tmp
            fi
            if [ $cosmic == y ]
            then
                z_score=`cat $WORKDIR/tmp | awk -F',' '{print $2}'`
            else
                z_score=0.000
            fi
        fi
    else                                                               #we have a compound
        z_score=0.000
    fi
    nge=`echo ${z_score} ${ONES} | awk '{printf "%.9f \n", $1 + $2}'`
    echo $line $z_score $nge >> $WORKDIR/receptors_contracted.tmp
done < $WORKDIR/receptors_contracted

tr -d $'\r' < $WORKDIR/receptors_contracted.tmp > $WORKDIR/receptors_contracted
rm $WORKDIR/receptors_contracted.tmp