test/read_all_write_all_seurat3.R

In ebi-gene-expression-group/workflowscriptscommon: Common Functions for Workflow Script Packages

suppressPackageStartupMessages(require(Seurat))
suppressPackageStartupMessages(require(scater))
suppressPackageStartupMessages(require(loomR))

args = commandArgs(trailingOnly=TRUE)
input_path = args[1]
input_format = args[2]

initial.options <- commandArgs(trailingOnly = FALSE)
file.arg.name <- "--file="
script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])

source(paste0(dirname(script.name),"/../R/seurat_io.R"))

print(paste0("Reading file ",input_path," for ", input_format," conversion to Seurat"))
params<-list(input_path = input_path, format = input_format)
if( input_format == "singlecellexperiment" ) {
  params$counts = "counts"
  params$data = "logcounts"
} else if( input_format == "loom" ) {
  params$loom_normalized_path = NULL
  params$loom_scaled_path = NULL
} else if( input_format == "seurat" ) {
  params$update_seurat_object = TRUE
}

so<-do.call(read_seurat3_object, params)
print(paste0("Read file."))

ext = list(loom="loom", singlecellexperiment="sce.rds", seurat="rds")

for(format in c("loom", "singlecellexperiment", "seurat")) {
  print(paste0("Writing file to format ", format))
  write_seurat3_object(so, format=format, output_path = paste0(input_path, ".", ext[format]))
}