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HiChIP/loopClassification.m

@@ -0,0 +1,63 @@
+clear all;
+
+cases = ["EE"; "EP"; "PP"];
+
+opts = delimitedTextImportOptions("NumVariables", 8);
+
+% Specify range and delimiter
+opts.DataLines = [1, Inf];
+opts.Delimiter = " ";
+
+% Specify column names and types
+opts.VariableNames = ["VarName1", "VarName2", "Var3", "Var4", "Var5", "Var6", "Var7", "Var8"];
+opts.SelectedVariableNames = ["VarName1", "VarName2"];
+opts.VariableTypes = ["string", "string", "string", "string", "string", "string", "string", "string"];
+
+% Specify file level properties
+opts.ExtraColumnsRule = "ignore";
+opts.EmptyLineRule = "read";
+opts.LeadingDelimitersRule = "ignore";
+
+% Specify variable properties
+opts = setvaropts(opts, ["VarName1", "VarName2", "Var3", "Var4", "Var5", "Var6", "Var7", "Var8"], "WhitespaceRule", "preserve");
+opts = setvaropts(opts, ["VarName1", "VarName2", "Var3", "Var4", "Var5", "Var6", "Var7", "Var8"], "EmptyFieldRule", "auto");
+
+EE = readmatrix(strcat("Merged.loops.Q0.01.",cases(1,1),".count"),opts);
+EP = readmatrix(strcat("Merged.loops.Q0.01.",cases(2,1),".count"),opts);
+PP = readmatrix(strcat("Merged.loops.Q0.01.",cases(3,1),".count"),opts);
+
+loops = readmatrix(strcat("Merged.loops.Q0.01.list"),'Delimiter','\t','FileType','text','OutputType','string');
+
+mat = strings(size(loops,1),5);
+mat(:,1) = loops;
+
+for i = 1:size(loops,1)
+    for j = 1:size(cases,1)
+        if j == 1
+            det = EE(strcmp(EE(:,2),loops(i,1)),:);
+        elseif j == 2
+            det = EP(strcmp(EP(:,2),loops(i,1)),:);
+        elseif j == 3
+            det = PP(strcmp(PP(:,2),loops(i,1)),:);
+        end
+
+        if size(det,1) > 0
+            mat(i,j+2) = det(1,1);
+        else
+            mat(i,j+2) = "0";
+        end
+    end
+
+    tuple = str2double(mat(i,3:5).');
+    if sum(tuple) == 0
+        mat(i,2) = "NA";
+    else
+        [~,idx] = max(tuple);
+        mat(i,2) = cases(idx,1);
+    end
+end
+
+for j = 1:size(cases,1)
+    submat = mat(strcmp(mat(:,2),cases(j,1)),1);
+    writematrix(submat,strcat("Merged.loops.Q0.01.",cases(j,1),".bedpe"),'FileType','text','Delimiter','\t');
+end

HiChIP/pairToPeak.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+bed="../bed"
+pair="../pair"
+loop="../loop"
+
+thres="100000"
+
+mkdir -p ${pair}/H3K27ac
+
+task() {
+awk '{printf "%s\t%s\t%s\t%s\t%s\t%s\t%s\t.\t%s\t%s\n", $2,$3,$3+1,$5,$6,$6+1,$1,$4,$7}' ${pair}/${1}/${1}.allValidPairs > ${pair}/${1}.validPairs.bedpe
+pairToBed -type both -a ${pair}/${1}.validPairs.bedpe -b ${bed}/H3K27ac.bed > ${pair}/H3K27ac/${1}.H3K27ac.validPairs.bedpe
+pairToBed -type both -a ${pair}/H3K27ac/${1}.H3K27ac.validPairs.bedpe -b ${bed}/H3K27ac.Enhancer.bed > ${pair}/H3K27ac/${1}.H3K27ac.EE.validPairs.bedpe
+pairToBed -type xor -a ${pair}/H3K27ac/${1}.H3K27ac.validPairs.bedpe -b ${bed}/H3K27ac.Enhancer.bed > ${pair}/H3K27ac/${1}.H3K27ac.EP.validPairs.bedpe
+pairToBed -type both -a ${pair}/H3K27ac/${1}.H3K27ac.validPairs.bedpe -b ${bed}/H3K27ac.Promoter.bed > ${pair}/H3K27ac/${1}.H3K27ac.PP.validPairs.bedpe
+}
+
+for file in WTCI KOCI
+do
+task "${file}" &
+done
+printf "Running...\n"
+wait
+printf "Completed\n"