Ingest a `Seurat`, `SingleCellExperiment`, or `SummarizedExperiment` object to a SOMA

ingest-soma.R

#!/usr/bin/env Rscript

suppressPackageStartupMessages(library(tiledbsoma))
suppressPackageStartupMessages(library(argparser))

parser <- argparser::arg_parser("", hide.opts = TRUE)
parser <- argparser::add_argument(
  parser = parser,
  arg = '--input',
  help = "Input Seurat, SingleCellExperiment, or SummarizedExperiment object as Rds",
  type = "character",
  nargs = 1L
)
parser <- argparser::add_argument(
  parser = parser,
  arg = '--output',
  help = "URI for output SOMA",
  type = "character",
  nargs = 1L
)
parser <- argparser::add_argument(
  parser = parser,
  arg = '--verbosity',
  help = "spdl verbosity level",
  default = "info",
  type = "character",
  nargs = 1L
)
parser <- argparser::add_argument(
  parser = parser,
  arg = '--resume',
  help = "Ingest in resume-mode",
  flag = TRUE
)

argv <- commandArgs(trailingOnly = TRUE)
if (!length(argv)) {
  print(parser)
  stop("No arguments provided", call. = FALSE)
}

args <- argparser::parse_args(parser = parser, argv = argv)
if (any(is.na(c(args$input, args$output)))) {
  stop("'--input' and '--output' are required", call. = FALSE)
}

spdl::set_level(args$verbosity)

if (!file.exists(args$input) || tolower(tools::file_ext(args$input)) != 'rds') {
  stop("'--input' must be an Rds file")
}

message("Reading input object from Rds")
obj <- readRDS(args$input)
if (!inherits(obj, c('Seurat', 'SingleCellExperiment', 'SummarizedExperiment'))) {
  stop("'--input' must be a `Seurat`, `SingleCellExperiment`, or `SummarizedExperiment` object")
}

uri <- tiledbsoma::write_soma(
  x = obj,
  uri = args$output,
  ingest_mode = ifelse(args$resume, yes = "resume", no = "write")
)

cat(uri, "\n", file = stdout())
message("Done")