add previously used scripts (mostly were deprecated), and need to be clean

#PBS -S /bin/bash

#PBS -q ser

#PBS -l nodes=1:ppn=1

#PBS -m a

#PBS -j oe

#PBS -N example_resolutionk_hicPlotMatrix

#PBS -o work_folder/experiment/example_resolutionk_hicPlotMatrix.log

source /home/bio-fangc/local/juicer/hic_essential_files/environment.sh

/home/bio-fangc/local/miniconda3/bin/computeMatrix scale-regions -S /home/bio-fangc/Data/UM/ChIP-seq/chip/GSM717393_maptags_AR_2H_CHV006.bed.sorted.bigwig -R ${hicexplorer_tad_data_folder}/DMSO_DHT_KR_resolutionk_boundaries.bed --beforeRegionStartLength 3000 --regionBodyLength 10000 --afterRegionStartLength 3000 --skipZeros -o /scratch/2020-08-01/chaos/Casodex/data_analysis/AR_to_boarder/AR_2h_DMSO_DHT_KR_resolutionk_boundaries_matrix.mat.gz

/home/bio-fangc/local/miniconda3/bin/computeMatrix -S /home/bio-fangc/Data/UM/ChIP-seq/chip/GSM717392_maptags_AR_0H_CHV005.bed.sorted.bigwig -R ${hicexplorer_tad_data_folder}/DMSO_EtOH_KR_resolutionk_boundaries.bed --beforeRegionStartLength 3000 --regionBodyLength 10000 --afterRegionStartLength 3000 --skipZeros -o /scratch/2020-08-01/chaos/Casodex/data_analysis/AR_to_boarder/AR_2h_DMSO_EtOH_KR_resolutionk_boundaries_matrix.mat.gz

#PBS -S /bin/bash

#PBS -q cal-s

#PBS -l nodes=1:ppn=24

#PBS -m a

#PBS -j oe

#PBS -N examplek_correlation

#PBS -o work_folder/experiment/examplek_correlation.log

source /home/bio-fangc/local/juicer/hic_essential_files/environment.sh

source activate 3dgenome

hicCorrelate --threads 24 -m ${cool_folder}/*_KR_examplek.cool --plotFileFormat pdf --plotNumbers --chromosomes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --threads 24 -oh ${correlation_folder}/examplek_correlation_heatmap.pdf -os ${correlation_folder}/examplek_correlation_scatter.pdf

#PBS -S /bin/bash

#PBS -q cal-s

#PBS -l nodes=1:ppn=24

#PBS -m a

#PBS -j oe

#PBS -N DL

source /home/bio-fangc/local/juicer/hic_essential_files/environment.sh

cat $sample_without_rep_list | while read j

do

	cat $sample_without_rep_list | while read k

	do

		if [ $j != $k ]

			then

				$juicer_tools hiccupsdiff -k KR ${hic_folder}/${j}.hic ${hic_folder}/${k}.hic ${hiccups_loop_folder}/${j}/${j}_merged_loops.bedpe ${hiccups_loop_folder}/${k}/${k}_merged_loops.bedpe ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops

				mv ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/file1 ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/${j}

				mv ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/file2 ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/${k}

				mv ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/differential_loops1.bedpe ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/${j}_unique_loops.bedpe

				mv ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/differential_loops2.bedpe ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/${k}_unique_loops.bedpe

				ls ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/${j}/ | while read i;

				do

					mv ${i} ${j}_${i}

				done

				ls ${hiccups_loop_folder}/Differential_Loops/${j}_${k}_Differential_Loops/${k}/ | while read i;

				do

					mv ${i} ${k}_${i}

				done

		fi

	done

done

#PBS -S /bin/bash

#PBS -q ser

#PBS -l nodes=1:ppn=1

#PBS -m a

#PBS -j oe

#PBS -N Eigenvector

 source /home/bio-fangc/local/juicer/hic_essential_files/environment.sh

cat $resolution_list_eigenvector | while read k

do

	mkdir ${eigenvector_folder}/${k}k ${eigenvector_corrected_folder}/${k}k

	cat $sample_without_rep_list | while read i

	do 

		cat $chr_list_all | while read j

		do

			$juicer_tools eigenvector -p KR ${hic_folder}/${i}.hic $j BP ${k}000  | awk '(NR>2){print $0}' >  ${eigenvector_folder}/${k}k/${i}_chr${j}_eigenvector_KR_${k}k

			sed -i 's/NaN/0/g' ${eigenvector_folder}/${k}k/${i}_chr${j}_eigenvector_KR_${k}k

			cp ${eigenvector_folder}/${k}k/${i}_chr${j}_eigenvector_KR_${k}k ${eigenvector_corrected_folder}/${k}k/${i}_chr${j}_eigenvector_KR_${k}k

			paste ${genedensity_folder}/${k}k/genedensity_${k}k_chr${j}.bed ${eigenvector_corrected_folder}/${k}k/${i}_chr${j}_eigenvector_KR_${k}k > ${eigenvector_corrected_folder}/${k}k/${i}_chr${j}_eigenvector_KR_${k}k_with_genesdensity

			cat ${eigenvector_corrected_folder}/${k}k/${i}_chr${j}_eigenvector_KR_${k}k_with_genesdensity | awk -vI=$i -vJ=$j -vK=$k 'BEGIN{sumPos=0;sumNeg=0;pos=0;neg=0}{if($6>0&&$6!="NaN"){pos++;sumPos+=$5}else if($6<0&&$6!="NaN"){neg++;sumNeg+=$5}}END{print I"_chr"J"_eigenvector_KR_"K"k","pos",sumPos,pos,sumPos/pos,"neg",sumNeg,neg,sumNeg/neg,"pos-neg",sumPos/pos-sumNeg/neg}' >> ${eigenvector_corrected_folder}/${k}k/average_gene_density_${k}k.txt

		done

	done

done

Rscript ${hic_essential_files}/eigenvector_correction.R

cat $resolution_list_eigenvector | while read k

do

	/bin/rm -rf ${eigenvector_corrected_folder}/${k}k/*_with_genesdensity

done

Rscript ${hic_essential_files}/eigenvector_plot.R

#PBS -S /bin/bash

#PBS -q cal-s

#PBS -l nodes=1:ppn=24

#PBS -m a

#PBS -j oe

#PBS -N file_convert

source /home/bio-fangc/local/juicer/hic_essential_files/environment.sh

source activate 3dgenome

cat $sample_all_list | while read i

do

{

	hicConvertFormat -m ${hic_folder}/${i}.hic --inputFormat hic --outputFormat cool --correction_name KR -o ${cool_folder}/${i}_KR.cool -r 2500000 1000000 500000 250000 100000 50000 25000 10000 5000 1000 

}

done

cat $sample_all_list | while read i

do

{

	hicConvertFormat -m ${hic_folder}/${i}.hic --inputFormat hic --outputFormat cool --correction_name KR -o ${cool_folder}/${i}_KR.cool

}

done

sleep 20m

cat $sample_all_list | while read i

do

	cat $resolution_list_all | while read j

	do

		mv ${cool_folder}/${i}_KR_${j}000.cool ${cool_folder}/${i}_KR_${j}k.cool

	done

done

cat $sample_all_list | while read i

do

	cat $resolution_list_all | while read j

	do

	{

		hicConvertFormat -m ${cool_folder}/${i}_KR_${j}k.cool  --inputFormat cool --outputFormat h5 -o  ${h5_folder}/${i}_KR_${j}k.h5

	}

	done

done