Added source Matlab code for reference

matlab/independent/processxls.m

@@ -0,0 +1,81 @@
+function [data, component_mat, popnames] = processxls(filename)
+%
+% a bug in line 64-68 was fixed
+data = [];
+component_mat = [];
+popnames = [];
+try
+    if ispc
+        [A,B] = xlsread(filename);
+    else
+        [A,B] = myxlsread(filename);
+    end
+catch
+    display('*** ERROR: Wrong Excel format');
+    return
+end
+
+if size(A,2)~=1   % more than one columns containing numeric ST values
+    display('*** ERROR: multiple columns of numeric values');
+    data = []; component_mat = []; popnames = [];
+    return
+end
+
+if size(A,1)~=size(B,1)-1
+    display('*** ERROR: Wrong format');
+    data = []; component_mat = []; popnames = [];   
+    return
+end
+
+B = deblank(B); % remove any trailing blanks
+nstrains = size(B,1)-1;
+nheader = size(B,2);
+for i = 1:nheader
+    if strcmpi('ST',B{1,i}) ix_ST = i; end
+    if strcmpi('Strain', B{1,i}) || strcmpi('Isolate',B{1,i})
+        ix_Strain = i; 
+    end
+end
+if ~exist('ix_ST') 
+    display('*** ERROR: ST column needed');
+    data = []; component_mat = []; popnames = [];
+    return
+end
+
+if ~exist('ix_Strain')
+    ix_gene = setdiff([1:nheader],ix_ST);
+else
+    ix_gene = setdiff([1:nheader],[ix_ST ix_Strain]);
+end
+    
+ngenes = length(ix_gene);
+
+C = cell(nstrains,ngenes);
+if ~isempty(A)
+    for i=1:nstrains
+        B{i+1,ix_ST}=num2str(A(i));
+        for j=1:ngenes
+            C{i,j}=uint16(i_encode_n(B{i+1,ix_gene(j)})); % save the memory.
+        end
+    end
+end
+genesize=cellfun('size',C(1,:),2);
+data=cell2mat(C);
+data=[data uint16([1:nstrains]')]; 
+component_mat = zeros(ngenes,max(genesize));
+cum = cumsum(genesize);
+component_mat(1,[1:genesize(1)]) = [1:cum(1)];
+for i=2:ngenes
+    component_mat(i,[1:genesize(i)]) = [(cum(i-1)+1):cum(i)];
+end
+
+if ~exist('ix_Strain')
+    popnames = num2cell(B([2:end],ix_ST));
+else  % store the strain names only
+    popnames = num2cell(B([2:end],ix_Strain)); 
+end
+popnames(:,2)=num2cell([1:nstrains]');
+
+display('---------------------------------------------------');
+display(['# of strains: ', num2str(nstrains)]);
+display(['# of genes: ', num2str(ngenes)]);