81 lines
No EOL
2.1 KiB
Matlab
81 lines
No EOL
2.1 KiB
Matlab
function [data, component_mat, popnames] = processxls(filename)
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%
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% a bug in line 64-68 was fixed
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data = [];
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component_mat = [];
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popnames = [];
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try
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if ispc
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[A,B] = xlsread(filename);
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else
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[A,B] = myxlsread(filename);
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end
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catch
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display('*** ERROR: Wrong Excel format');
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return
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end
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if size(A,2)~=1 % more than one columns containing numeric ST values
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display('*** ERROR: multiple columns of numeric values');
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data = []; component_mat = []; popnames = [];
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return
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end
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if size(A,1)~=size(B,1)-1
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display('*** ERROR: Wrong format');
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data = []; component_mat = []; popnames = [];
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return
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end
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B = deblank(B); % remove any trailing blanks
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nstrains = size(B,1)-1;
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nheader = size(B,2);
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for i = 1:nheader
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if strcmpi('ST',B{1,i}) ix_ST = i; end
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if strcmpi('Strain', B{1,i}) || strcmpi('Isolate',B{1,i})
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ix_Strain = i;
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end
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end
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if ~exist('ix_ST')
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display('*** ERROR: ST column needed');
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data = []; component_mat = []; popnames = [];
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return
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end
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if ~exist('ix_Strain')
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ix_gene = setdiff([1:nheader],ix_ST);
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else
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ix_gene = setdiff([1:nheader],[ix_ST ix_Strain]);
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end
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ngenes = length(ix_gene);
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C = cell(nstrains,ngenes);
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if ~isempty(A)
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for i=1:nstrains
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B{i+1,ix_ST}=num2str(A(i));
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for j=1:ngenes
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C{i,j}=uint16(i_encode_n(B{i+1,ix_gene(j)})); % save the memory.
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end
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end
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end
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genesize=cellfun('size',C(1,:),2);
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data=cell2mat(C);
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data=[data uint16([1:nstrains]')];
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component_mat = zeros(ngenes,max(genesize));
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cum = cumsum(genesize);
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component_mat(1,[1:genesize(1)]) = [1:cum(1)];
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for i=2:ngenes
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component_mat(i,[1:genesize(i)]) = [(cum(i-1)+1):cum(i)];
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end
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if ~exist('ix_Strain')
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popnames = num2cell(B([2:end],ix_ST));
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else % store the strain names only
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popnames = num2cell(B([2:end],ix_Strain));
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end
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popnames(:,2)=num2cell([1:nstrains]');
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display('---------------------------------------------------');
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display(['# of strains: ', num2str(nstrains)]);
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display(['# of genes: ', num2str(ngenes)]); |