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sc_readh5adfile.m
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sc_readh5adfile.m
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function [X, g, b, filenm] = sc_readh5adfile(filenm)
%Read H5AD file
% https://anndata.readthedocs.io/en/latest/fileformat-prose.html
% https://www.mathworks.com/help/matlab/hdf5-files.html
% http://scipy-lectures.org/advanced/scipy_sparse/csc_matrix.html
% https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices
% https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3489183
% h5file='GSM3489183_IPF_01_filtered_gene_bc_matrices_h5.h5';
X = [];
g = [];
b = [];
if nargin < 1 || isempty(filenm)
[filenm, pathname] = uigetfile( ...
{'*.h5ad', 'H5AD Files (*.h5ad)'; ...
'*.*', 'All Files (*.*)'}, ...
'Pick a H5AD file');
if isequal(filenm, 0), return; end
filenm = fullfile(pathname, filenm);
end
if exist(filenm, 'file') ~= 2, error('File Not Found.'); end
% fw = gui.gui_waitbar_adv;
hinfo = h5info(filenm);
idx = find(strcmp(strtrim(string(char(hinfo.Groups.Name))), "/X"));
%data=h5read(filenm,[hinfo.Groups(idx).Name,'/data']);
%indices=h5read(filenm,[hinfo.Groups(idx).Name,'/indices']);
%indptr=h5read(filenm,[hinfo.Groups(idx).Name,'/indptr']);
data = pkg.e_guessh5field(filenm, {'/X/'}, {'data'}, true);
if isequal(data(1:5), round(data(1:5)))
indices = pkg.e_guessh5field(filenm, {'/X/'}, {'indices'}, true);
indptr = pkg.e_guessh5field(filenm, {'/X/'}, {'indptr'}, true);
else
disp('/X has been transformed/normalized, but SCGEATOOL needs raw counts. Reading /raw/X');
data = pkg.e_guessh5field(filenm, {'/raw/X/'}, {'data'}, true);
indices = pkg.e_guessh5field(filenm, {'/raw/X/'}, {'indices'}, true);
indptr = pkg.e_guessh5field(filenm, {'/raw/X/'}, {'indptr'}, true);
end
% idx=find(strcmp(strtrim(string(char(hinfo.Groups.Name))),"/raw"));
% data=h5read(filenm,[hinfo.Groups(idx).Groups(1).Name,'/data']);
% indices=h5read(filenm,[hinfo.Groups(idx).Groups(1).Name,'/indices']);
% indptr=h5read(filenm,[hinfo.Groups(idx).Groups(1).Name,'/indptr']);
idx2 = find(strcmp(strtrim(string(char(hinfo.Groups(idx).Attributes.Name))), "shape"));
shape = double(hinfo.Groups(idx).Attributes(idx2).Value);
g = pkg.e_guessh5field(filenm, {'/var/'}, {'_index', 'gene_ids', 'gene_name'}, false);
if isempty(g) || isscalar(unique(strlength(g))) % suggesting ENSEMBLE ID
disp('Reading /var/feature_name/categories');
gx = pkg.e_guessh5field(filenm, {'/raw/var/feature_name/', ...
'/var/feature_name/'}, {'categories'}, false);
if ~isempty(gx)
g = gx;
end
end
if isempty(g), warning('Genename is not assigned.'); end
% idx=find(strcmp(strtrim(string(char(hinfo.Groups.Name))),"/var"));
% try
% g=h5read(filenm,[hinfo.Groups(idx).Name,'/_index']);
% catch
% try
% g=h5read(filenm,[hinfo.Groups(idx).Name,'/gene_ids']);
% catch
% try
% g=h5read(filenm,[hinfo.Groups(idx).Name,'/gene_name']);
% catch
% warning('GENELIST not found.');
% end
% end
% end
b = pkg.e_guessh5field(filenm, {'/obs/'}, {'_index', 'barcodes','cell_id','CellID'});
if isempty(b), warning('Barcode is not assigned.'); end
% try
% barcodes=h5read(filenm,[hinfo.Groups.Groups(1).Name,'/barcodes']);
% catch
% try
% barcodes=h5read(filenm,[hinfo.Groups(2).Name,'/index']);
% %barcodes=h5read(filenm,[hinfo.Groups(1).Name,'/barcodes']);
% catch
% try
% barcodes=h5read(filenm,'/obs/_index');
% catch
% warning('BARCODES not found.');
% end
% end
% end
X = spalloc(shape(2), shape(1), length(data));
for k = 1:length(indptr) - 1
i = indptr(k) + 1:indptr(k+1);
y = indices(i) + 1;
X(y, k) = data(i);
end
g = deblank(string(g));
% genelist=strings(length(g),1);
% for k=1:length(g)
% genelist(k)=string(g(k).data);
% end
% gui.gui_waitbar_adv(fw);
end
% a=h5read(filenm,'/obs/seurat_clusters')
% a=h5read(filenm,'/var/_index')
% a=h5read(filenm,'/obs/annotation')
%{
function i_tryread
try
g=h5read(filenm,[hinfo.Groups(idx).Name,'/_index']);
catch
end
end
%}