create_NSC_numbers_file

source $vini_dir/sourceme

if [ $cell_line == SF268 ] ; then  #map COSMIC to NCI-60 cell names
   cell_line=SF-268
fi
if [ $cell_line == SF295 ] ; then
   cell_line=SF-295
fi
if [ $cell_line == SF539 ] ; then
   cell_line=SF-539
fi
if [ $cell_line == SNB75 ] ; then
   cell_line=SNB-75
fi
if [ $cell_line == T47D ] ; then
   cell_line=T-47D
fi
if [ $cell_line == TK10 ] ; then
   cell_line=TK-10
fi
if [ $cell_line == MCF-7 ] ; then
   cell_line=MCF7
fi
if [ $cell_line == T47D ] ; then
   cell_line=T-47D
fi
if [ $cell_line == HT-29 ] ; then
   cell_line=HT29
fi
if [ $cell_line == LOXIMVI ] ; then
   cell_line=LOX
fi



#https://dtp.cancer.gov/dtpstandard/cancerscreeningdata/index.jsp

#(Chemical name that starts with AND 5 dose data)

#download GI50.zip from https://wiki.nci.nih.gov/display/NCIDTPdata/NCI-60+Growth+Inhibition+Data to $vini_dir/database
#AgentInfo.txt is downloaded from https://ctep.cancer.gov/protocoldevelopment/codes_values.htm#agent

if [ ! -e AgentInfo ]
then
    echo -n "Downloading AgentInfo file..."
    curl -o tmp -Ls https://ctepcore.nci.nih.gov/webobjs/CTEPWebsite/AgentInfo.html 
    python $HOME/.local/bin/html2text tmp > AgentInfo
    echo "done."
fi

if [ ! -e GI50.csv ]
then
    echo -n "Downloading GI50.zip, please wait."
    wget -O GI50.zip https://wiki.nci.nih.gov/download/attachments/147193864/GI50.zip?version=5
    unzip -o GI50.zip
    rm GI50.zip
fi

echo -n "Creating NSC_numbers file..."
> tmp
while read -r line                                           
do
    drugname=`echo $line | awk -F',' '{print $1}'`                   
    grep -w "$drugname" AgentInfo > lines
    nolines=`wc -l < lines`
    if  [ $nolines -eq $NULL ]
    then 
        echo "drug" $drugname "not found in AgentInfo file"
    else
        if [ $nolines -eq $ONES ]
        then
            NSC_NUMBER=`cat lines | awk  'NF>1{print $NF}'`
            echo "NSC number for drug" $drugname "found:" $NSC_NUMBER
        else
            echo "Found several NSC numbers for drug" $drugname "in AgentInfo file:" ; echo
            cat lines ; echo
            NSC_NUMBER=`head -1 lines`
            NSC_NUMBER=`echo $NSC_NUMBER | awk  'NF>1{print $NF}'`
            echo "NSC number" $NSC_NUMBER "will be used." ; echo ; sleep 4
        fi
        printf "%s%s%s%s\n" "$drugname" "," " " "$NSC_NUMBER" >> tmp
    fi
done <  $vini_dir/ligands/ligands_list 
sed -e "s/\r//g" tmp > NSC_numbers               #remove ^M from file


grep $cell_line $vini_dir/database/GI50.csv > tmp    #extract cell line entries from GI50.csv file
sed -e "s/\r//g" tmp > $vini_dir/database/${cell_line}_GI50        #remove ^M


> tmp                       #remove entries without values from the ${cell_line}_GI50 file
while read -r line
do
    drugname=`echo $line | awk -F','  '{print $2}'`
    grep -w $drugname $vini_dir/database/${cell_line}_GI50 > lines
    nolines=`wc -l < lines`
    if  [ $nolines -gt $NULL ]
    then
        echo $line >> tmp
    fi
done < $vini_dir/database/NSC_numbers



if  [ -s tmp ]
then
    mv tmp $vini_dir/database/NSC_numbers
else
    echo "no drugs in your ligands_list have been evaluated with NCI-60 GI protocol!"
    echo "SLEM values will be computed but the correlation analysis with GI50 data will be not performed!"
fi
rm lines