SINGE shell script and separation of GLG_Instance and Aggregate functions

code/Aggregate.m

@@ -0,0 +1,25 @@
+function Aggregate(genefile,Data,outdir)
+load(genefile);
+
+Str = Data;
+Str(Str=='.') = 'p';
+
+lind = max(max(strfind(Str,filesep)),0);
+if isempty(lind)
+    lind = 0;
+end
+mind = length(Str);
+
+Str = Str(lind+1:mind);
+Agg = Modified_Borda_Aggregation(Str,outdir);
+
+ranked_edges = adjmatrix2edgelist(Agg,gene_list);
+[influence,ind] = sort(sum(Agg,2),'descend');
+gene_influence = [cell2table(gene_list(ind)) array2table(influence)];
+gene_influence.Properties.VariableNames{1} = 'Gene_Name';
+ranked_edgesw = ranked_edges;
+ranked_edgesw.SCINGE_Score = floor(ranked_edgesw.SCINGE_Score*10^5)/10^5;
+gene_influencew = gene_influence;
+gene_influencew.influence = floor(gene_influencew.influence*10^5)/10^5;
+writetable(ranked_edgesw,fullfile(outdir,'SCINGE_Ranked_Edge_List.txt'),'WriteVariableNames',true,'WriteRowNames',false,'Delimiter','\t');
+writetable(gene_influencew,fullfile(outdir,'SCINGE_Gene_Influence.txt'),'WriteVariableNames',true,'WriteRowNames',false,'Delimiter','\t');

code/SCINGE.m

@@ -12,31 +12,13 @@
 % Outputs:
 % ranked_edges = ranked list of gene interactions with corresponding SCINGE scores
 % gene_influence = ranked lists of regulators (genes) with corresponding SCINGE influence
-SCINGE_version = '0.2.0';
+SCINGE_version = '0.3.0';
 display(SCINGE_version);
 for rep = 1:num_replicates
     for ii = 1:length(param_list)
-        GLG_Instance(Data,'lambda',param_list{ii}.lambda,'dT',param_list{ii}.dT,'num_lags',param_list{ii}.num_lags,'kernel_width',param_list{ii}.kernel_width,'prob_zero_removal',param_list{ii}.prob_zero_removal,'replicate',rep,'ID',param_list{ii}.ID,'outdir',outdir,'family',param_list{ii}.family,'prob_remove_samples',param_list{ii}.prob_remove_samples,'date',param_list{ii}.date);
+        GLG_Instance(Data,'--lambda',param_list{ii}.lambda,'--dT',param_list{ii}.dT,'--num_lags',param_list{ii}.num_lags,'--kernel_width',param_list{ii}.kernel_width,'--prob_zero_removal',param_list{ii}.prob_zero_removal,'--replicate',rep,'--ID',param_list{ii}.ID,'--outdir',outdir,'--family',param_list{ii}.family,'--prob_remove_samples',param_list{ii}.prob_remove_samples,'--date',param_list{ii}.date);
     end
 end
-Str = Data;
-Str(Str=='.') = 'p';
 
-lind = max(max(strfind(Str,filesep)),0);
-mind = length(Str);
-if isempty(mind)||(mind<lind)
-    mind = length(Str);
-end
-Str = Str(lind+1:mind);
-Agg = Modified_Borda_Aggregation(Str,outdir);
+Aggregate(gene_list,Data,outdir);
 
-ranked_edges = adjmatrix2edgelist(Agg,gene_list);
-[influence,ind] = sort(sum(Agg,2),'descend');
-gene_influence = [cell2table(gene_list(ind)) array2table(influence)];
-gene_influence.Properties.VariableNames{1} = 'Gene_Name';
-ranked_edgesw = ranked_edges;
-ranked_edgesw.SCINGE_Score = floor(ranked_edgesw.SCINGE_Score*10^5)/10^5;
-gene_influencew = gene_influence;
-gene_influencew.influence = floor(gene_influencew.influence*10^5)/10^5;
-writetable(ranked_edgesw,fullfile(outdir,'SCINGE_Ranked_Edge_List.txt'),'WriteVariableNames',true,'WriteRowNames',false,'Delimiter','\t');
-writetable(gene_influencew,fullfile(outdir,'SCINGE_Gene_Influence.txt'),'WriteVariableNames',true,'WriteRowNames',false,'Delimiter','\t');

code/parseParams.m

@@ -1,4 +1,12 @@
 function params = parseParams(Data,varargin)
+for ii = 1:length(varargin)
+    temp = varargin{ii};
+    if numel(temp)>2
+        if strcmpi(temp(1:2),'--')
+            varargin{ii} = temp(3:end);
+        end
+    end
+end
 p = inputParser;
 def_lambda = 0.01;
 def_dT = 1;

standalone_SCINGE.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+Data=$1
+outdir=$3
+gene_list=$2
+hypefile=hyperparameters.txt
+while read arg||[ -n "$arg" ]; do 
+    ./run_GLG_Instance.sh v94 $Data --outdir $outdir $arg
+done < $hypefile
+
+./run_Aggregate.sh v94 $gene_list $Data $outdir