autoscript

j=$(pwd)
for filename in $j/$1/*; do
    basename "${filename}"
    
    # If a SNP set is not provided, then use all SNPs
    # Otherwise filter out the SNP set
    if [ -z "$3" ]
        then
            ./plink --23file $filename --recode --out me >run.log 2>error.log
            ./plink --bfile $2 --make-bed --out reference_panel/temp_panel >>run.log 2>>error.log
    else
            ./plink --23file $filename --extract $3 --recode --out me >run.log 2>error.log
            ./plink --bfile $2 --extract $3 --make-bed --out reference_panel/temp_panel >>run.log 2>>error.log
    fi
    
    ./ancestry temp_panel
    

    open ancestry.png
    echo 
    echo "Press enter to start next run: "
    read input

    # Remove old analysis files
    rm -f me*
done

# House keeping
rm -f reference_panel/temp_panel*