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GeneNames_Extract.m
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GeneNames_Extract.m
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clear all;
close all;
Out_Stages=1; % {1,2,3,4,5,...}
DatasetNum=1;
FileRun = ['Run',num2str(DatasetNum)]; %Run1, Run2, Run3, Run4, Run5, Run6,...
genesCompressed = 'no'; % 'no', 'yes'
Directory = ['Models/',FileRun,'/Stage1'];
FILES = {'PDX_Paclitaxel','PDX_Gemcitabine','PDX_Cetuximab','PDX_Erlotinib','TCGA_Docetaxel','TCGA_Cisplatin','TCGA_Gemcitabine'};
GeneFileNames=FILES{DatasetNum};
if Out_Stages > 0
%RUN1 or Run2
cd(Directory)
if strcmp(lower(genesCompressed),'yes')==1
Stage1 = load('Genes_compressed.mat');
Genes_compressed = Stage1.Genes_compressed;
if isfile('Genes_PerClass_compressed.mat')==1
Gcomp = load('Genes_PerClass_compressed.mat');
Gcomp = Gcomp.Gcomp;
end
else
Stage1 = load('Genes.mat');
Genes = Stage1.Genes;
if isfile('Genes_PerClass.mat')==1
G = load('Genes_PerClass.mat');
G = G.G;
end
end
% This is the output of Stage 1, using this line will execute Stage 2
Num=1;
if Out_Stages > 1
cd ../Stage2
if strcmp(lower(genesCompressed),'yes')==1
Stage2 = load('Genes_compressed.mat');
Genes_compressed = Stage1.Genes_compressed(Stage2.Genes_compressed);
if isfile('Genes_PerClass_compressed.mat')==1
Gcomp = load('Genes_PerClass_compressed.mat');
Gcomp = Gcomp.Gcomp;
for j=1:length(Gcomp)
Gcomp{j} = Stage1.Genes_compressed(Gcomp{j});
end
end
else
Stage2 = load('Genes.mat');
Genes = Stage1.Genes(Stage2.Genes);
if isfile('Genes_PerClass.mat')==1
G = load('Genes_PerClass.mat');
G = G.G;
for j=1:length(G)
G{j} = Stage1.Genes(G{j});
end
end
end
% This is the output of Stage 2, using this line will execute Stage 3
Num=2;
end
if Out_Stages > 2
cd ../Stage3
if strcmp(lower(genesCompressed),'yes')==1
Stage3 = load('Genes_compressed.mat');
Genes_compressed = Stage1.Genes_compressed(Stage2.Genes_compressed(Stage3.Genes_compressed));
if isfile('Genes_PerClass_compressed.mat')==1
Gcomp = load('Genes_PerClass_compressed.mat');
Gcomp = Gcomp.Gcomp;
for j=1:length(Gcomp)
Gcomp{j} = Stage1.Genes_compressed(Stage2.Genes_compressed(Gcomp{j}));
end
end
else
Stage3 = load('Genes.mat');
Genes = Stage1.Genes(Stage2.Genes(Stage3.Genes));
if isfile('Genes_PerClass.mat')==1
G = load('Genes_PerClass.mat');
G = G.G;
for j=1:length(G)
G{j} = Stage1.Genes(Stage2.Genes(G{j}));
end
end
end
%This is the output of Stage 3, using this line will execute Stage 4 (NotTested)
Num=3;
end
if Out_Stages > 3
cd ../Stage4
if strcmp(lower(genesCompressed),'yes')==1
Stage4 = load('Genes_compressed.mat');
Genes_compressed = Stage1.Genes_compressed(Stage2.Genes_compressed(Stage3.Genes_compressed(Stage4.Genes_compressed)));
if isfile('Genes_PerClass_compressed.mat')==1
Gcomp = load('Genes_PerClass_compressed.mat');
Gcomp = Gcomp.Gcomp;
for j=1:length(Gcomp)
Gcomp{j} = Stage1.Genes_compressed(Stage2.Genes_compressed(Stage3.Genes_compressed(Gcomp{j})));
end
end
else
Stage4 = load('Genes.mat');
Genes = Stage1.Genes(Stage2.Genes(Stage3.Genes(Stage4.Genes)));
if isfile('Genes_PerClass.mat')==1
G = load('Genes_PerClass.mat');
G = G.G;
for j=1:length(G)
G{j} = Stage1.Genes(Stage2.Genes(Stage3.Genes(G{j})));
end
end
end
%This is the output of Stage 4, using this line will execute Stage 5 (NotTested)
Num=4;
end
if Out_Stages > 4
cd ../Stage5
if strcmp(lower(genesCompressed),'yes')==1
Stage5 = load('Genes_compressed.mat');
Genes_compressed = Stage1.Genes_compressed(Stage2.Genes_compressed(Stage3.Genes_compressed(Stage4.Genes_compressed(Stage5.Genes_compressed))));
if isfile('Genes_PerClass_compressed.mat')==1
Gcomp = load('Genes_PerClass_compressed.mat');
Gcomp = Gcomp.Gcomp;
for j=1:length(Gcomp)
Gcomp{j} = Stage1.Genes_compressed(Stage2.Genes_compressed(Stage3.Genes_compressed(Stage4.Genes_compressed(Gcomp{j}))));
end
end
else
Stage5 = load('Genes.mat');
Genes = Stage1.Genes(Stage2.Genes(Stage3.Genes(Stage4.Genes(Stage5.Genes))));
if isfile('Genes_PerClass.mat')==1
G = load('Genes_PerClass.mat');
G = G.G;
for j=1:length(G)
G{j} = Stage1.Genes(Stage2.Genes(Stage3.Genes(Stage4.Genes(G{j}))));
end
end
end
%This is the output of Stage 4, using this line will execute Stage 5
Num=5;
end
if Out_Stages > 5
cd ../Stage6
if strcmp(lower(genesCompressed),'yes')==1
Stage6 = load('Genes_compressed.mat');
Genes_compressed = Stage1.Genes_compressed(Stage2.Genes_compressed(Stage3.Genes_compressed(Stage4.Genes_compressed(Stage5.Genes_compressed(Stage6.Genes_compressed)))));
if isfile('Genes_PerClass_compressed.mat')==1
Gcomp = load('Genes_PerClass_compressed.mat');
Gcomp = Gcomp.Gcomp;
for j=1:length(Gcomp)
Gcomp{j} = Stage1.Genes_compressed(Stage2.Genes_compressed(Stage3.Genes_compressed(Stage4.Genes_compressed(Stage5.Genes_compressed(Gcomp{j})))));
end
end
else
Stage6 = load('Genes.mat');
Genes = Stage1.Genes(Stage2.Genes(Stage3.Genes(Stage4.Genes(Stage5.Genes(Stage6.Genes)))));
if isfile('Genes_PerClass.mat')==1
G = load('Genes_PerClass.mat');
G = G.G;
for j=1:length(G)
G{j} = Stage1.Genes(Stage2.Genes(Stage3.Genes(Stage4.Genes(Stage5.Genes(G{j})))));
end
end
end
%This is the output of Stage 5, using this line will execute Stage 6 (NotTested)
Num=6;
end
cd ../../../
end
%if strcmp(lower(genesCompressed),'yes')==1
% unix(['mv GeneList.txt Unique_Genes.txt']);
%else
% unix(['mv GeneList_UnCmprss.txt Unique_Genes.txt']);
%end
File = [Directory(1:end-1),num2str(Num)];
if strcmp(lower(genesCompressed),'yes')==1
GeneNames(Genes_compressed,1,GeneFileNames);
unix(['cp GeneList.txt ',File]);
%unix(['cp Unique_Genes.txt ',File]);
if exist('Gcomp')==1
GeneNames(Gcomp,1,GeneFileNames);
unix(['mv GenePerClass*.txt ',File]);
end
else
GeneNames(Genes,0,GeneFileNames);
unix(['cp GeneList_UnCmprss.txt ',File]);
%unix(['cp Unique_Genes.txt ',File]);[
if exist('G')==1
GeneNames(G,0,GeneFileNames);
unix(['mv GeneUnCmprssPerClass_*.txt ',File]);
end
end
unix(['mkdir ',File,'/',[FileRun,'Stage',num2str(Out_Stages)]]);
unix(['mv ',File,'/*.txt ',File,'/',[FileRun,'Stage',num2str(Out_Stages)],'/']);
unix(['tar -cvf ',File,'/',[FileRun,'Stage',num2str(Out_Stages)],'.tar ',File,'/',[FileRun,'Stage',num2str(Out_Stages)],'/']);
unix(['gzip ',File,'/',[FileRun,'Stage',num2str(Out_Stages)],'.tar']);
if exist('GeneFileNames')==1
unix(['cp ',File,'/',[FileRun,'Stage',num2str(Out_Stages),'.tar.gz'],' ',File,'/',GeneFileNames,'.tar.gz']);
end