Download FASTQ Files.

Usage

DownloadFastq(
  gsm.df,
  out.folder = NULL,
  download.method = c("download.file", "ascp", "wget"),
  quiet = FALSE,
  timeout = 3600,
  ascp.path = NULL,
  max.rate = "300m",
  parallel = TRUE,
  use.cores = NULL,
  wget.path = NULL,
  format.10x = TRUE,
  remove.raw = TRUE
)

Arguments

gsm.df: Dataframe contains GSM and Run numbers, obtained from ExtractRun.
out.folder: Output folder. Default: NULL (current working directory).
download.method: Method to download fastq files, chosen from "download.file", "ascp" and "wget". Default: "download.file".
quiet: Logical value, whether to show downloading progress. Used when download.method is "download.file". Default: FALSE (show).
timeout: Maximum request time. Used when download.method is "download.file" or "wget". Default: 3600.
ascp.path: Path to ascp (/path/bin/ascp), please ensure that the relative path of asperaweb_id_dsa.openssh file (/path/bin/ascp/../etc/asperaweb_id_dsa.openssh). Default: NULL (conduct automatic detection).
max.rate: Max transfer rate. Used when download.method is "ascp". Default: 300m.
parallel: Logical value, whether to download parallelly. Default: TRUE.
use.cores: The number of cores used. Default: NULL (the minimum value of nrow(gsm.df) and parallel::detectCores()).
wget.path: Path to wget. Default: NULL (conduct automatic detection).
format.10x: Logical value, whether to format split fastqs to 10x standard format. Default: TRUE.
remove.raw: Logical value, whether to remove old split fastqs (unformatted), used when format.10x is TRUE. Default: TRUE.

Value

Dataframe contains failed gsm.df of NULL.

Examples

if (FALSE) { # \dontrun{
GSE130636.runs <- ExtractRun(acce = "GSE130636", platform = "GPL20301")
# a small test
GSE130636.runs <- GSE130636.runs[GSE130636.runs$run %in% c("SRR9004325", "SRR9004326"), ]
# use download.file
download.file.res <- DownloadFastq(
  gsm.df = gsm.df, out.folder = "/path/to/output", remove.raw = TRUE,
  download.method = "download.file", parallel = TRUE, use.cores = 2
)
# use ascp
ascp.res <- DownloadFastq(
  gsm.df = gsm.df, out.folder = "/path/to/output", remove.raw = TRUE,
  download.method = "ascp", ascp.path = "~/.aspera/connect/bin/ascp",
  parallel = TRUE, use.cores = 2
)
# use wget
wget.res <- DownloadFastq(
  gsm.df = gsm.df, out.folder = "/path/to/output", remove.raw = TRUE,
  download.method = "wget", wget.path = "/usr/bin/wget",
  parallel = TRUE, use.cores = 2
)
} # }