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Summarize_KO_Results_timeseries.m~
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% Summerize results of Single Gene Deletion
% Find mat files output from essentiality analysis with SKO
model_files = dir('./KO_data/timeseries/');
model_files = {model_files.name};
model_files = model_files(find(startsWith(model_files,'SKO')));
T_SKO = cell2table(cell(0,5));
for m=1:numel(model_files)
filepath = model_files{m};
X = load(strcat('./KO_data/timeseries/',filepath)) ;
models = fieldnames(X) ;
%models = models(find(contains(models,'_cov')));
SKO_genes = models(find(startsWith(models,'SKO_')));
SKO_safe = SKO_genes(find(contains(SKO_genes,'_safe')));
SKO_toxic = SKO_genes(find(contains(SKO_genes,'_toxic')));
SKO_unk = SKO_genes(find(contains(SKO_genes,'_unk')));
SKO_cov = models(find(contains(models,'genes_cov')));
N = numel(SKO_safe)/1;
for k=1:N
grp = strsplit(filepath,'_'); %strsplit(SKO_toxic{k*2},'_')
grp = strjoin(grp(2:3),'_');
generic_model = strsplit(filepath,'_');
generic_model = generic_model(4);
generic_model = cell2mat(generic_model);
sko_safe = strjoin( X.(SKO_safe{k}),',');
sko_toxic = strjoin(X.(SKO_toxic{k})',',');
sko_cov = X.(SKO_cov{k});
xx = X.(SKO_unk{k})
sko_unk = strjoin(string(X.(SKO_unk{k}))',',')
model_ctl = X.('model_ctl');
if isstruct(model_ctl) == 0
sko_unk = strjoin(sko_cov';
sko_safe = '0';
sko_toxic = '0';
end
x = table({grp},{generic_model}, {sko_safe},{sko_toxic},{sko_unk});
x.Properties.VariableNames = [{'Var1'},{'Var2'},{'Var3'},{'Var4'},{'Var5'}];
T_SKO = [T_SKO ; x];
end
end
for xx=1:numel(model_files)
filepath = model_files{xx};
X = load(strcat('KO_data/timeseries/',filepath)) ;
models = fieldnames(X) ;
%models = models(find(contains(models,'_cov')));
SKO_genes = models(find(startsWith(models,'SKO_')));
SKO_ctl = SKO_genes(find(contains(SKO_genes,'_ctl')));
SKO_cov = SKO_genes(find(contains(SKO_genes,'_cov')));
SKO_unk = SKO_genes(find(contains(SKO_genes,'_unk')))
N = numel(SKO_cov);
filepath = filepath(5:end);
for k=1:N
grp = strsplit(filepath,'_'); %strsplit(SKO_toxic{k*2},'_')
grp = strjoin(grp(1:2),'_'); %grp(3)
%grp = cell2mat(grp); %grp{1, 1}
sko_ctl = X.(SKO_ctl{k});
sko_cov = X.(SKO_cov{k});
model_ctl = X.('model_ctl');
sko_toxic = strjoin(intersect(sko_cov,sko_ctl),',');
sko_safe = strjoin(setdiff(sko_cov,sko_ctl),',');
sko_unk = '0';
% search for infected models with mock model, to assign their genes
% as unkown safety
if isstruct(model_ctl) == 0
sko_unk = sko_safe;
sko_safe = '0';
sko_toxic = '0';
end
generic_model = strsplit(filepath,'_');
generic_model = generic_model(3);
generic_model = cell2mat(generic_model)
x = table({grp},{generic_model}, {sko_safe},{sko_toxic},{sko_unk});
x.Properties.VariableNames = [{'Var1'},{'Var2'},{'Var3'},{'Var4'},{'Var5'}];
T_SKO = [T_SKO ; x];
end
end
T_SKO.Properties.VariableNames = [{'Series'},{'RECON'},{'SKO_Safe'},{'SKO_Toxic'},{'SKO_Unknown'}]
writetable(T_SKO,'KO_data/timeseries_SKO_All.csv');
% Summerize results of Double Gene Deletion
model_files = dir('./KO_data/timeseries/');
model_files = {model_files.name};
model_files = model_files(find(startsWith(model_files,'DKO')));
T_DKO = cell2table(cell(0,5));
for i=1:numel(model_files)
filepath = model_files{i};
X = load(strcat('KO_data/timeseries/',filepath)) ;
models = fieldnames(X) ;
%models = models(find(endsWith(models,'_cov')));
DKO_genes = models(find(startsWith(models,'DKO_')));
DKO_safe = DKO_genes(find(contains(DKO_genes,'_safe')));
DKO_toxic = DKO_genes(find(contains(DKO_genes,'_toxic')));
DKO_non_ess = DKO_genes(find(contains(DKO_genes,'_non_ess')));
DKO_syn = DKO_genes(find(contains(DKO_genes,'_syn')));
DKO_both = DKO_genes(find(contains(DKO_genes,'_both')));
N = numel(DKO_safe);
for k=1:N
grp = strsplit(filepath,'_'); %strsplit(SKO_toxic{k*2},'_')
grp = string(strjoin(grp(2:3),'_')); %grp(3)
dKO_safe = X.(DKO_safe{k})
dKO_toxic = X.(DKO_toxic{k})
if istable(dKO_toxic)~=1
dKO_toxic = table(string(dKO_toxic(:,1)),string(dKO_toxic(:,2)));
dKO_toxic.Properties.VariableNames = [{'c'},{'r'}];
end
if istable(dKO_safe)~=1
dKO_safe = table(string(dKO_safe(:,1)),string(dKO_safe(:,2)));
dKO_safe.Properties.VariableNames = [{'c'},{'r'}];
end
%dKO_non_ess = X.(DKO_non_ess{k})
%dKO_syn = X.(DKO_syn{k})
dKO = [dKO_safe;dKO_toxic];
safety = [repmat('Safe_',size(dKO_safe,1),1);repmat('Toxic',size(dKO_toxic,1),1)];
if size(safety,1)==1
safety = char(safety);
safety = {safety};
safety = table(safety)
%safety.Properties.VariableNames = {'safety'}
else
safety = table(safety);
end
generic_model = strsplit(filepath,'_');
generic_model = generic_model(4);
generic_model = cell2mat(generic_model)
if size(safety,1)==1
grp = grp{1}
%generic_model = table(string([repmat(generic_model(1,3),size(dKO,1),1)]));
%generic_model =generic_model)
grp = repmat(grp,size(dKO,1),1);
grp= table(string(grp));
else
generic_model = table([repmat(generic_model(1),size(dKO,1),1)]);
grp = repmat(grp,size(dKO,1),1);
end
%x = horzcat(grp, string(dKO),table2cell( safety),table2cell(generic_model));
x = table( grp,dKO(:,1),dKO(:,2),table2cell(safety),table2cell(generic_model));
%x = table(x,5);
%x1 = x.x;
x.Properties.VariableNames = [{'Var1'},{'Var2'},{'Var3'},{'Var4'},{'Var5'}];
T_DKO = [T_DKO ; x];
end
end
T_DKO.Properties.VariableNames = [{'Series'},{'Gene1'},{'Gene2'},{'Safe_Toxic'},{'RECON_Model'}]
% x = horzcat(T_DKO(:,1),T_DKO(:,3),T_DKO(:,2),T_DKO(:,4),T_DKO(:,5));
% T_DKO = [T_DKO ; x];
T_DKO.Gene2 = T_DKO.Gene2.r
T_DKO.Gene1 = T_DKO.Gene1.c
% Series = T_DKO{:,1};
% T_DKO.Series = Series;
writetable(T_DKO,'KO_data/timeseries_DKO_All.csv');