@@ -48,6 +48,10 @@ exportSCEtoAnnData <- function(sce,

             " correct Python environment.")

     return(sce)}

+  if (!is(SummarizedExperiment::assay(sce), 'dgCMatrix')) {

+    SummarizedExperiment::assay(sce) <- .convertToMatrix(SummarizedExperiment::assay(sce))

+  }

+

   annData <- .sce2adata(sce,useAssay)

   fileName <- paste0(sample,".h5ad")

   filePath <- file.path(outputDir,fileName)

@@ -269,11 +269,23 @@ distinctColors <- function(n, hues = c("red", "cyan", "orange", "blue",

 .convertToMatrix <- function(x) {

   cn <- colnames(x)

   rn <- rownames(x)

+  limit <- (2^32/2-1)

+  dimN <- dim(x)

+  chuS <- floor(floor(limit/dimN[1]))

+  chuN <- ceiling(dimN[2]/chuS)

+  Mat <- list()

-  x <- methods::as(x, "dgCMatrix")

+  for (i in 1:chuN) {

+    startT <- Sys.time()

+    start <- (i-1)*chuS + 1

+    end <- min(i*chuS, dimN[2])

+    Mat[[i]] <- methods::as(x[, start:end], "Matrix")

+    endT <- Sys.time()

+    print(endT - startT)

+  }

+  x <- do.call(base::cbind, Mat)

   colnames(x) <- cn

   rownames(x) <- rn

-  

   return(x)

 }

@@ -214,6 +214,10 @@ if (!is.null(mergedDropletSCE)) {

     ## Export to flatfile

     fn <- file.path(directory, samplename, "FlatFile", "Droplets")

     exportSCEtoFlatFile(mergedDropletSCE, outputDir = fn)

+

+    ## Export to Python AnnData

+    fn <- file.path(directory, samplename, "Python", "Droplets")

+    exportSCEtoAnnData(mergedDropletSCE, outputDir=fn, compression='gzip', sample=samplename)

 }

 if (!is.null(mergedFilteredSCE)) {

     ## Export to R        

@@ -223,4 +227,9 @@ if (!is.null(mergedFilteredSCE)) {

     ## Export to flatfile    

     fn <- file.path(directory, samplename, "FlatFile", "FilteredCells")

     exportSCEtoFlatFile(mergedFilteredSCE, outputDir = fn)

+

+    ## Export to Python AnnData

+    fn <- file.path(directory, samplename, "Python", "FilteredCells")

+    exportSCEtoAnnData(mergedFilteredSCE, outputDir=fn, compression='gzip', sample=samplename)

+

 }    

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