download.ebi: Faster download of fastq files

In JokingHero/ORFik: Open Reading Frames in Genomics

Faster download of fastq files

Description

Uses ftp download from vol1 drive on EBI ftp server, for faster download of ERR, SRR or DRR files. But does not support subsetting or custom settings of files!

Usage

download.ebi(
  info,
  outdir,
  rename = TRUE,
  ebiDLMethod = "auto",
  timeout = 5000,
  BPPARAM = bpparam()
)

Arguments

info	character vector of only SRR numbers or a data.frame with SRA metadata information including the SRR numbers in a column called "Run" or "SRR". Can be SRR, ERR or DRR numbers. If only SRR numbers can not rename, since no additional information is given.
outdir	directory to store runs, files are named by default (rename = TRUE) by information from SRA metadata table, if (rename = FALSE) named according to SRR numbers.
rename	logical or character, default TRUE (Auto guess new names). False: Skip renaming. A character vector of equal size as files wanted can also be given. Priority of renaming from the metadata is to check for unique names in the LibraryName column, then the sample_title column if no valid names in LibraryName. If new names found and still duplicates, will add "_rep1", "_rep2" to make them unique. If no valid names, will not rename, that is keep the SRR numbers, you then can manually rename files to something more meaningful.
ebiDLMethod	character, default "auto". Which download protocol to use in download.file when using ebi ftp download. Sometimes "curl" is might not work (the default auto usually), in those cases use wget. See "method" argument of ?download.file, for more info.
timeout	5000, how many seconds before killing download if still active? Will overwrite global option until R session is closed. Increase value if you are on a very slow connection or downloading a large dataset.
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers

Value

character, full filepath of downloaded files

See Also

Other sra: browseSRA(), download.SRA(), download.SRA.metadata(), get_bioproject_candidates(), install.sratoolkit(), rename.SRA.files()

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.