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Devel #10

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merged 13 commits into from
Jul 19, 2023
Merged

Devel #10

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8cf0587
Updating cellranger upload
irzamsarfraz May 30, 2023
7da3d4c
Updated file system issues with cellranger import on server
irzamsarfraz Jun 23, 2023
f46657b
Minor fix
irzamsarfraz Jun 23, 2023
9e7c3b9
Added optional metrics summary file option for cellranger
irzamsarfraz Jul 14, 2023
cf05413
Added option for metrics summary file for cellranger
irzamsarfraz Jul 14, 2023
6bcfeef
Added starSolo import from files
irzamsarfraz Jul 15, 2023
701fc5e
Updates to data import
irzamsarfraz Jul 15, 2023
0e63689
Updates to seqc import
irzamsarfraz Jul 16, 2023
e13e43b
Cosmetic changes to import ui
irzamsarfraz Jul 18, 2023
65dd1a3
Merge pull request #707 from mingl1997/devel
joshua-d-campbell Jul 18, 2023
e614278
Merge branch 'devel' into dir-test2
irzamsarfraz Jul 19, 2023
72bef02
Merge pull request #4 from irzamsarfraz/dir-test2
irzamsarfraz Jul 19, 2023
5d25a28
Merge pull request #709 from irzamsarfraz/devel
joshua-d-campbell Jul 19, 2023
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199 changes: 198 additions & 1 deletion R/importMultipleSources.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,32 +41,229 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
delayedArray = delayedArray
)
}
} else if (entry$type == "cellRanger3_files") {

# get current tempDir by shiny
mytempdir <- tempdir(check=TRUE)

if(dir.exists(mytempdir)){
# get uploaded filepaths
matrixFilePath <- entry$params$assayFile
barcodesFilePath <- entry$params$annotFile
featuresFilePath <- entry$params$featureFile
metricsFilePath <- entry$params$summaryFile

# rename to original names
file.rename(matrixFilePath, paste0(dirname(matrixFilePath), "/matrix.mtx.gz"))
file.rename(barcodesFilePath, paste0(dirname(barcodesFilePath), "/barcodes.tsv.gz"))
file.rename(featuresFilePath, paste0(dirname(featuresFilePath), "/features.tsv.gz"))
if(!is.null(metricsFilePath)){
file.rename(metricsFilePath, paste0(dirname(metricsFilePath), "/metrics_summary.csv"))
}

# create a sample folder
dir.create(paste0(mytempdir, "/cellranger/"))
if(!is.null(metricsFilePath)){
dir.create(paste0(mytempdir, "/cellranger/outs"))
}

# move files to this sample folder
file.copy(paste0(dirname(matrixFilePath), "/matrix.mtx.gz"), paste0(mytempdir, "/cellranger/matrix.mtx.gz"))
file.copy(paste0(dirname(barcodesFilePath), "/barcodes.tsv.gz"), paste0(mytempdir, "/cellranger/barcodes.tsv.gz"))
file.copy(paste0(dirname(featuresFilePath), "/features.tsv.gz"), paste0(mytempdir, "/cellranger/features.tsv.gz"))
if(!is.null(metricsFilePath)){
file.copy(paste0(dirname(metricsFilePath), "/metrics_summary.csv"), paste0(mytempdir, "/cellranger/outs/metrics_summary.csv"))
}

# make object
newSce <- importCellRangerV3Sample(dataDir = paste0(mytempdir, "/cellranger/"))

# delete sample folder
unlink(paste0(mytempdir, "/cellranger/"), recursive = TRUE)
}

} else if (entry$type == "starSolo") {
newSce <- importSTARsolo(
STARsoloDirs = entry$params$STARsoloDirs,
samples = entry$params$samples,
STARsoloOuts = entry$params$STARsoloOuts,
delayedArray = delayedArray
)
} else if (entry$type == "starSolo_files") {

# get current tempDir by shiny
mytempdir <- tempdir(check=TRUE)

if(dir.exists(mytempdir)){
# get uploaded filepaths
matrixFilePath <- entry$params$assayFile
barcodesFilePath <- entry$params$annotFile
featuresFilePath <- entry$params$featureFile
# metricsFilePath <- entry$params$summaryFile

# rename to original names
file.rename(matrixFilePath, paste0(dirname(matrixFilePath), "/matrix.mtx"))
file.rename(barcodesFilePath, paste0(dirname(barcodesFilePath), "/barcodes.tsv"))
file.rename(featuresFilePath, paste0(dirname(featuresFilePath), "/features.tsv"))
# if(!is.null(metricsFilePath)){
# file.rename(metricsFilePath, paste0(dirname(metricsFilePath), "/metrics_summary.csv"))
# }

# create a sample folder
dir.create(paste0(mytempdir, "/Solo.out/"))
dir.create(paste0(mytempdir, "/Solo.out/Gene/"))
dir.create(paste0(mytempdir, "/Solo.out/Gene/filtered"))
# if(!is.null(metricsFilePath)){
# dir.create(paste0(mytempdir, "/cellranger/outs"))
# }

# move files to this sample folder
file.copy(paste0(dirname(matrixFilePath), "/matrix.mtx"), paste0(mytempdir, "/Solo.out/Gene/filtered/matrix.mtx"))
file.copy(paste0(dirname(barcodesFilePath), "/barcodes.tsv"), paste0(mytempdir, "/Solo.out/Gene/filtered/barcodes.tsv"))
file.copy(paste0(dirname(featuresFilePath), "/features.tsv"), paste0(mytempdir, "/Solo.out/Gene/filtered/features.tsv"))
# if(!is.null(metricsFilePath)){
# file.copy(paste0(dirname(metricsFilePath), "/metrics_summary.csv"), paste0(mytempdir, "/cellranger/outs/metrics_summary.csv"))
# }

# make object
newSce <- importSTARsolo(STARsoloDirs = paste0(mytempdir, "/Solo.out"), samples = "sample1")

# delete sample folder
unlink(paste0(mytempdir, "/Solo.out/"), recursive = TRUE)

# newSce <- importSTARsolo(
# STARsoloDirs = entry$params$STARsoloDirs,
# samples = entry$params$samples,
# STARsoloOuts = entry$params$STARsoloOuts,
# delayedArray = delayedArray
# )
}
} else if (entry$type == "busTools") {
newSce <- importBUStools(
BUStoolsDirs = entry$params$BUStoolsDirs,
samples = entry$params$samples,
delayedArray = delayedArray
)
} else if (entry$type == "busTools_files") {
# get current tempDir by shiny
mytempdir <- tempdir(check=TRUE)

if(dir.exists(mytempdir)){
# get uploaded filepaths
matrixFilePath <- entry$params$assayFile
barcodesFilePath <- entry$params$annotFile
featuresFilePath <- entry$params$featureFile
# metricsFilePath <- entry$params$summaryFile

# rename to original names
file.rename(matrixFilePath, paste0(dirname(matrixFilePath), "/genes.mtx"))
file.rename(barcodesFilePath, paste0(dirname(barcodesFilePath), "/genes.barcodes.txt"))
file.rename(featuresFilePath, paste0(dirname(featuresFilePath), "/genes.genes.txt"))
# if(!is.null(metricsFilePath)){
# file.rename(metricsFilePath, paste0(dirname(metricsFilePath), "/metrics_summary.csv"))
# }

# create a sample folder
dir.create(paste0(mytempdir, "/bus_output/"))

# move files to this sample folder
file.copy(paste0(dirname(matrixFilePath), "/genes.mtx"), paste0(mytempdir, "/bus_output/genes.mtx"))
file.copy(paste0(dirname(barcodesFilePath), "/genes.barcodes.txt"), paste0(mytempdir, "/bus_output/genes.barcodes.txt"))
file.copy(paste0(dirname(featuresFilePath), "/genes.genes.txt"), paste0(mytempdir, "/bus_output/genes.genes.txt"))

# make object
newSce <- importBUStools(BUStoolsDirs = paste0(mytempdir, "/bus_output"), samples = "sample1")

# delete sample folder
unlink(paste0(mytempdir, "/bus_output/"), recursive = TRUE)
}
} else if (entry$type == "seqc") {
newSce <- importSEQC(
seqcDirs = entry$params$seqcDirs,
samples = entry$params$samples,
prefix = entry$params$prefix,
delayedArray = delayedArray
)
} else if (entry$type == "seqc_files") {
# get current tempDir by shiny
mytempdir <- tempdir(check=TRUE)

if(dir.exists(mytempdir)){
# get uploaded filepaths
readCountsLocation <- entry$params$readCountsLocation
moleculeCountsLocation <- entry$params$moleculeCountsLocation
barcodesLocation <- entry$params$barcodesLocation
genesLocation <- entry$params$genesLocation

# rename to original names
file.rename(readCountsLocation, paste0(dirname(readCountsLocation), "/seqc_sparse_read_counts.mtx"))
file.rename(moleculeCountsLocation, paste0(dirname(moleculeCountsLocation), "/seqc_sparse_molecule_counts.mtx"))
file.rename(barcodesLocation, paste0(dirname(barcodesLocation), "/seqc_sparse_counts_barcodes.csv"))
file.rename(genesLocation, paste0(dirname(genesLocation), "/seqc_sparse_counts_genes.csv"))

# create a sample folder
dir.create(paste0(mytempdir, "/seqc/"))

# move files to this sample folder
file.copy(paste0(dirname(readCountsLocation), "/seqc_sparse_read_counts.mtx"), paste0(mytempdir, "/seqc/seqc_sparse_read_counts.mtx"))
file.copy(paste0(dirname(moleculeCountsLocation), "/seqc_sparse_molecule_counts.mtx"), paste0(mytempdir, "/seqc/seqc_sparse_molecule_counts.mtx"))
file.copy(paste0(dirname(barcodesLocation), "/seqc_sparse_counts_barcodes.csv"), paste0(mytempdir, "/seqc/seqc_sparse_counts_barcodes.csv"))
file.copy(paste0(dirname(genesLocation), "/seqc_sparse_counts_genes.csv"), paste0(mytempdir, "/seqc/seqc_sparse_counts_genes.csv"))

# make object
newSce <- importSEQC(seqcDirs = paste0(mytempdir, "/seqc"), samples = "sample1", prefix = "seqc")

# delete sample folder
unlink(paste0(mytempdir, "/seqc/"), recursive = TRUE)
}
} else if (entry$type == "optimus") {
newSce <- importOptimus(
OptimusDirs = entry$params$OptimusDirs,
samples = entry$params$samples,
delayedArray = delayedArray
)
} else if (entry$type == "optimus_files") {
# get current tempDir by shiny
mytempdir <- tempdir(check=TRUE)

if(dir.exists(mytempdir)){
# get uploaded filepaths
matrixLocation <- entry$params$matrixLocation
colIndexLocation <- entry$params$colIndexLocation
rowIndexLocation <- entry$params$rowIndexLocation
cellMetricsLocation <- entry$params$cellMetricsLocation
geneMetricsLocation <- entry$params$geneMetricsLocation
emptyDropsLocation <- entry$params$emptyDropsLocation

# rename to original names
file.rename(matrixLocation, paste0(dirname(matrixLocation), "/sparse_counts.npz"))
file.rename(colIndexLocation, paste0(dirname(colIndexLocation), "/sparse_counts_col_index.npy"))
file.rename(rowIndexLocation, paste0(dirname(rowIndexLocation), "/sparse_counts_row_index.npy"))
file.rename(cellMetricsLocation, paste0(dirname(cellMetricsLocation), "/merged-cell-metrics.csv.gz"))
file.rename(geneMetricsLocation, paste0(dirname(geneMetricsLocation), "/merged-gene-metrics.csv.gz"))
file.rename(emptyDropsLocation, paste0(dirname(emptyDropsLocation), "/empty_drops_result.csv"))

# create a sample folder
dir.create(paste0(mytempdir, "/optimus/"))
dir.create(paste0(mytempdir, "/optimus/call-MergeCountFiles/"))
dir.create(paste0(mytempdir, "/optimus/call-MergeCellMetrics/"))
dir.create(paste0(mytempdir, "/optimus/call-MergeGeneMetrics/"))
dir.create(paste0(mytempdir, "/optimus/call-RunEmptyDrops/"))

# move files to this sample folder
file.copy(paste0(dirname(matrixLocation), "/sparse_counts.npz"), paste0(mytempdir, "/optimus/call-MergeCountFiles/sparse_counts.npz"))
file.copy(paste0(dirname(colIndexLocation), "/sparse_counts_col_index.npy"), paste0(mytempdir, "/optimus/call-MergeCountFiles/sparse_counts_col_index.npy"))
file.copy(paste0(dirname(rowIndexLocation), "/sparse_counts_row_index.npy"), paste0(mytempdir, "/optimus/call-MergeCountFiles/sparse_counts_row_index.npy"))
file.copy(paste0(dirname(cellMetricsLocation), "/merged-cell-metrics.csv.gz"), paste0(mytempdir, "/optimus/call-MergeCellMetrics/merged-cell-metrics.csv.gz"))
file.copy(paste0(dirname(geneMetricsLocation), "/merged-gene-metrics.csv.gz"), paste0(mytempdir, "/optimus/call-MergeGeneMetrics/merged-gene-metrics.csv.gz"))
file.copy(paste0(dirname(emptyDropsLocation), "/empty_drops_result.csv"), paste0(mytempdir, "/optimus/call-RunEmptyDrops/empty_drops_result.csv"))

# make object
newSce <- importOptimus(OptimusDirs = paste0(mytempdir, "/optimus"), samples = "sample1")

# delete sample folder
unlink(paste0(mytempdir, "/optimus/"), recursive = TRUE)
}
} else if (entry$type == "files") {
newSce <- importFromFiles(assayFile = entry$params$assayFile,
annotFile = entry$params$annotFile,
Expand Down Expand Up @@ -99,7 +296,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
}

# Begin Set Tags
if(entry$type %in% c("cellRanger2", "cellRanger3", "starSolo", "busTools", "seqc", "optimus", "example")){
if(entry$type %in% c("cellRanger2", "cellRanger3", "starSolo", "busTools", "seqc", "optimus", "example", "cellRanger3_files", "starSolo_files", "busTools_files", "optimus_files", "seqc_files")){
newSce <- expSetDataTag(
inSCE = newSce,
assayType = "raw",
Expand Down
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