Circos Plot.sh

#Install Circos
conda install circos
#Install dependency modules
cpanm -v Carp Clone Config::General Cwd Data::Dumper Digest::MD5 File::Basename File::Spec::Functions File::Temp FindBin Font::TTF::Font GD GD::Polyline Getopt::Long IO::File List::MoreUtils List::Util Math::Bezier Math::BigFloat Math::Round Math::VecStat Memoize POSIX Params::Validate Pod::Usage Readonly Regexp::Common SVG Set::IntSpan Statistics::Basic Storable Sys::Hostname Text::Balanced Text::Format Time::HiRes

#Turn VCF Spots into number counts in region
for ID in $(ls | grep -P -o '.*(?=(.vcf))')
do
    if [ ! -f ${ID}.dat.txt ] ;then
        awk '/^#/ {next} {printf("%s\t%d\n",$1,$2-$2%10000);}' ${ID}.vcf | sort | uniq -c | awk '{printf("%s\t%s\t%d\t%s\n",$2,$3,$3+10000,$1);}' > ${ID}.dat.txt
    fi
done

for ID in $(ls | grep -P -o '.*(?=(.dat.txt))')
do
    if [ ! -f ${ID}.chrd.txt ] ;then
        echo process ${ID} changing chromosome id to name
        cp ${ID}.dat.txt ${ID}.chrd.txt
        pids="$pids $!"
        wait $pids
        while read ref_seq chr
        do
            #Convert ref_seq ID into chromosome number
            sed -i s/${ref_seq}/${chr}/g ${ID}.chrd.txt
            pids="$pids $!"
            wait $pids
        done < ref_chr.list
    fi
    if [ ! -f ${ID}.png ] ;then
        echo Create ${ID} config file for circos
        #Input the plot file and the max point
        maxpoint=$(sort -rnk4 ${ID}.chrd.txt | awk '!x[$2]++' | head -1 | cut -f 4)
        sed s/plotfileinput.txt/${ID}.chrd.txt/g vcf_density.conf > ${ID}_vcf_density.conf
        sed -i s/max_point_vale/${maxpoint}/g ${ID}_vcf_density.conf
        pids="$pids $!"
        wait $pids
        echo Drawing ${ID} circos plot
        circos -outputdir ./ -outputfile ${ID} -conf ${ID}_vcf_density.conf
        pids="$pids $!"
        wait $pids
    fi
    rm ${ID}.dat.txt
done