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calculateDNAmeInRegions.sh
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calculateDNAmeInRegions.sh
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!/bin/bash
# calculateDNAmeInRegions.sh
#########################
echo "\033[32m @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ \033[0m"
start=$(date +%Y-%m-%d\ %H:%M:%S)
echo "\033[32m BEGIN@ "$start" \033[0m"
echo "\033[32m enjoy~ \033[0m"
echo "\033[32m @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ @o@ \033[0m"
echo ""
#########################
help_info(){
echo "usage:"
echo "bash calculateDNAmeInRegions.sh <option>* [-x input_1] [-y input_2] [-r region] [-s strand] [-f fasta] [-c chrome_size] [-o output_path] [-p prefix]"
echo ""
echo "This file is for calculating DNA methylation level for given region (based on Bismark output)."
echo "Supporting one file or 2 replicates, strand specific or without strand."
echo ""
echo "Arguments:"
echo "-x Input DNAme file (bedMethyl file)."
echo "-y Input file for replicate 2 (if with replications)."
echo "-r The interested regions with uniq name on the 4th column."
echo " Should be strandard 6 column bed file."
echo "-s Logical parameter (1 or 0). "
echo " 1 means region file with strand Info, this code will considering strand while doing intersectBed."
echo "-f The genome fasta file."
echo "-c The chromosome size file."
echo "-o The path for output file."
echo "-p Prefix for intermediate files."
echo ""
echo "Any questions, please contact me."
echo " --Kaili Fan ([email protected])"
echo ""
}
if [ $# -lt 6 ];then
help_info
exit 1
fi
input_2="NA"
while getopts "x:y:r:s:f:c:o:p:" Arg
do
case $Arg in
x) input_1=$OPTARG;;
y) input_2=$OPTARG
echo "with replicates";;
r) region=$OPTARG;;
s) strand=$OPTARG;;
f) fasta=$OPTARG;;
c) chrome_size=$OPTARG;;
o) output_path=$OPTARG;;
p) prefix=$OPTARG;;
?) echo "Wrong parameter!!!"
exit 1;;
esac
done
#########################
cd ${output_path}
echo ${prefix}
# 1. count number of CpG sites
echo "counting CpG sites"
bedtools slop -i ${region} -g ${chrome_size} -b 1 > temp_${prefix}_region_add.bed ;
bedtools getfasta -fi ${fasta} -bed temp_${prefix}_region_add.bed > temp_${prefix}_fa.txt ;
cat temp_${prefix}_fa.txt | tr a-z A-Z | awk '{if(NR%2!=1){split($0,a,"CG");print length(a)-1}}' > ${prefix}_cg_count.txt ;
paste ${region} ${prefix}_cg_count.txt > ${prefix}_cg_count_merge.txt ;
if [ ${strand} == "1" ];then
echo "strand-specific" ;
if [ "$input_2" = "NA" ]; then
# 2. remove low coverage CpG sites
echo "remove CpG sites with less than 5 reads coverage" ;
aveMethy_1=`awk '{FS=OFS="\t"}{if($10>5){sum+=$11}}END{print sum/(100*NR)}' ${input_1}` ;
awk 'BEGIN{FS=OFS="\t"} {if($10>5){print $1,$2,$3,$4,$11/100,$6}}' ${input_1} > temp_${prefix}_raw_methy_1.txt ;
# 3. calculate DNA methylation level of given region in each file
echo "DNAme in files" ;
intersectBed -a ${prefix}_cg_count_merge.txt -b temp_${prefix}_raw_methy_1.txt -s -wa -wb | \
awk -v aveMethy="$aveMethy_1" 'BEGIN{FS=OFS="\t"}{sm[$4]+=$12;sn[$4]+=1}END{for(i in sm){if(sn[i]){print i,sn[i],sm[i]/sn[i]}else{print i,0,aveMethy}}}' \
> ${prefix}_CG_methy_count_1.txt ;
# 4. fix
echo "fix..." ;
awk '{FS=OFS="\t"}{if(NR==FNR){a[$1]=$2;b[$1]=$3}else{if($7==0){print $0,"NA"}else if(($7!=0)&&(a[$4]==0)){print $0,-0.1}else{print $0,b[$4]}}}' \
${prefix}_CG_methy_count_1.txt ${prefix}_cg_count_merge.txt > ${prefix}_cg_DNAme.txt ;
else
# 2. clean methyl data
echo "remove CpG sites with less than 5 reads coverage" ;
aveMethy_1=`awk '{FS=OFS="\t"}{if($10>5){sum+=$11}}END{print sum/(100*NR)}' ${input_1}` ;
awk 'BEGIN{FS=OFS="\t"} {if($10>5){print $1,$2,$3,$4,$11/100,$6}}' ${input_1} > temp_${prefix}_raw_methy_1.txt ;
aveMethy_2=`awk '{FS=OFS="\t"}{if($10>5){sum+=$11}}END{print sum/(100*NR)}' ${input_2}` ;
awk 'BEGIN{FS=OFS="\t"} {if($10>5){print $1,$2,$3,$4,$11/100,$6}}' ${input_2} > temp_${prefix}_raw_methy_2.txt ;
# 3. calculate DNA methylation level of given region in each file
echo "DNAme in files" ;
intersectBed -a ${prefix}_cg_count_merge.txt -b temp_${prefix}_raw_methy_1.txt -s -wa -wb | \
awk -v aveMethy="$aveMethy_1" 'BEGIN{FS=OFS="\t"}{sm[$4]+=$12;sn[$4]+=1}END{for(i in sm){if(sn[i]){print i,sn[i],sm[i]/sn[i]}else{print i,0,aveMethy}}}' \
> ${prefix}_CG_methy_count_1.txt ;
intersectBed -a ${prefix}_cg_count_merge.txt -b temp_${prefix}_raw_methy_2.txt -s -wa -wb | \
awk -v aveMethy="$aveMethy_2" 'BEGIN{FS=OFS="\t"}{sm[$4]+=$12;sn[$4]+=1}END{for(i in sm){if(sn[i]){print i,sn[i],sm[i]/sn[i]}else{print i,0,aveMethy}}}' \
> ${prefix}_CG_methy_count_2.txt ;
awk '{FS=OFS="\t"}{if(NR==FNR){a[$1]=$2;b[$1]=$3}else{m=($3+b[$1])/2; print $1,a[$1],b[$1],$2,$3,m}}' ${prefix}_CG_methy_count_1.txt \
${prefix}_CG_methy_count_2.txt > ${prefix}_CG_methy_count.txt ;
# 4. fix
echo "fix..." ;
awk '{FS=OFS="\t"}{if(NR==FNR){a[$4]=$7}else{if((a[$1]!=0)&&($2==0)&&($4==0)){print $1,-0.1}else if((a[$1]!=0)&&($2==0)&&($4!=0)){print $1,$5}else if((a[$1]!=0)&&($2!=0)&&($4==0)){print $1,$3}else{print $1,$6}}}' \
${prefix}_cg_count_merge.txt ${prefix}_CG_methy_count.txt > ${prefix}_CG_methy_count_fix.txt ;
awk '{FS=OFS="\t"}{if(NR==FNR){a[$1]=$2}else{if($4 in a){print $0,a[$4]}else{if($5==0){print $0,"NA"}else{print $0,-0.1}}}}' \
${prefix}_CG_methy_count_fix.txt ${prefix}_cg_count_merge.txt > ${prefix}_cg_DNAme.txt ;
fi
else
echo "without strand Info";
if [ "$input_2" = "NA" ]; then
# 2. remove low coverage CpG sites
echo "remove CpG sites with less than 5 reads coverage" ;
aveMethy_1=`awk '{FS=OFS="\t"}{if($10>5){sum+=$11}}END{print sum/(100*NR)}' ${input_1}` ;
awk 'BEGIN{FS=OFS="\t"} {if($10>5){print $1,$2,$3,$4,$11/100,$6}}' ${input_1} > temp_${prefix}_raw_methy_1.txt ;
# 3. calculate DNA methylation level of given region in each file
echo "DNAme in files" ;
intersectBed -a ${prefix}_cg_count_merge.txt -b temp_${prefix}_raw_methy_1.txt -wa -wb | \
awk -v aveMethy="$aveMethy_1" 'BEGIN{FS=OFS="\t"}{sm[$4]+=$12;sn[$4]+=1}END{for(i in sm){if(sn[i]){print i,sn[i],sm[i]/sn[i]}else{print i,0,aveMethy}}}' \
> ${prefix}_CG_methy_count_1.txt ;
# 4. fix
echo "fix..." ;
awk '{FS=OFS="\t"}{if(NR==FNR){a[$1]=$2;b[$1]=$3}else{if($7==0){print $0,"NA"}else if(($7!=0)&&(a[$4]==0)){print $0,-0.1}else{print $0,b[$4]}}}' \
${prefix}_CG_methy_count_1.txt ${prefix}_cg_count_merge.txt > ${prefix}_cg_DNAme.txt ;
else
# 2. clean methyl data
echo "remove CpG sites with less than 5 reads coverage" ;
aveMethy_1=`awk '{FS=OFS="\t"}{if($10>5){sum+=$11}}END{print sum/(100*NR)}' ${input_1}` ;
awk 'BEGIN{FS=OFS="\t"} {if($10>5){print $1,$2,$3,$4,$11/100,$6}}' ${input_1} > temp_${prefix}_raw_methy_1.txt ;
aveMethy_2=`awk '{FS=OFS="\t"}{if($10>5){sum+=$11}}END{print sum/(100*NR)}' ${input_2}` ;
awk 'BEGIN{FS=OFS="\t"} {if($10>5){print $1,$2,$3,$4,$11/100,$6}}' ${input_2} > temp_${prefix}_raw_methy_2.txt ;
# 3. calculate DNA methylation level of given region in each file
echo "DNAme in files" ;
intersectBed -a ${prefix}_cg_count_merge.txt -b temp_${prefix}_raw_methy_1.txt -wa -wb | \
awk -v aveMethy="$aveMethy_1" 'BEGIN{FS=OFS="\t"}{sm[$4]+=$12;sn[$4]+=1}END{for(i in sm){if(sn[i]){print i,sn[i],sm[i]/sn[i]}else{print i,0,aveMethy}}}' \
> ${prefix}_CG_methy_count_1.txt ;
intersectBed -a ${prefix}_cg_count_merge.txt -b temp_${prefix}_raw_methy_2.txt -wa -wb | \
awk -v aveMethy="$aveMethy_2" 'BEGIN{FS=OFS="\t"}{sm[$4]+=$12;sn[$4]+=1}END{for(i in sm){if(sn[i]){print i,sn[i],sm[i]/sn[i]}else{print i,0,aveMethy}}}' \
> ${prefix}_CG_methy_count_2.txt ;
awk '{FS=OFS="\t"}{if(NR==FNR){a[$1]=$2;b[$1]=$3}else{m=($3+b[$1])/2; print $1,a[$1],b[$1],$2,$3,m}}' ${prefix}_CG_methy_count_1.txt \
${prefix}_CG_methy_count_2.txt > ${prefix}_CG_methy_count.txt ;
# 4. fix
echo "fix..." ;
awk '{FS=OFS="\t"}{if(NR==FNR){a[$4]=$7}else{if((a[$1]!=0)&&($2==0)&&($4==0)){print $1,-0.1}else if((a[$1]!=0)&&($2==0)&&($4!=0)){print $1,$5}else if((a[$1]!=0)&&($2!=0)&&($4==0)){print $1,$3}else{print $1,$6}}}' \
${prefix}_cg_count_merge.txt ${prefix}_CG_methy_count.txt > ${prefix}_CG_methy_count_fix.txt ;
awk '{FS=OFS="\t"}{if(NR==FNR){a[$1]=$2}else{if($4 in a){print $0,a[$4]}else{if($5==0){print $0,"NA"}else{print $0,-0.1}}}}' \
${prefix}_CG_methy_count_fix.txt ${prefix}_cg_count_merge.txt > ${prefix}_cg_DNAme.txt ;
fi
fi
rm temp_${prefix}_*
echo ""
echo ""
echo "\033[32m Cheers!!!✌️ ✌️ ✌️ \033[0m"
echo ""
echo ""
#########################
echo "\033[32m ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^\033[0m"
end=$(date +%Y-%m-%d\ %H:%M:%S)
echo "\033[32m END@ "$end" \033[0m"
echo "\033[32m Time used: $((${SECONDS} / 3600))h $((${SECONDS} / 60))m \033[0m"
echo "\033[32m ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^ ^m^\033[0m"