#!/usr/bin/env Rscript
suppressPackageStartupMessages(require(Seurat))
args = commandArgs(trailingOnly=TRUE)
input_path = args[1]
output_path = 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"))
sc_matrix <- Read10X(data.dir = input_path,
unique.features = TRUE,
gene.column = 2)
seurat_object <- CreateSeuratObject(sc_matrix)
# For Loom export to work
seurat_object <- FindVariableFeatures(object = seurat_object)
write_seurat3_object(seurat_object, format="seurat", output_path = output_path)
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