getFASTQfile: Download SRA fastq files from EBI ENA through ftp or fasp
In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

getFASTQfile

R Documentation

Download SRA fastq files from EBI ENA through ftp or fasp

Description

This function downloads SRA fastq data files through ftp or fasp from EBI ENA site for a given list of SRA accessions.

Usage

getFASTQfile( in_acc, sra_con, destDir = getwd(), srcType = 'ftp', makeDirectory = FALSE, method = 'curl', ascpCMD = NULL)

Arguments

`in_acc`	character vector of SRA accessions that could be be in one or more SRA sata types: study, sample, experiment and/or run.
`sra_con`	connection to the SRAmetadb SQLite database
`destDir`	destination directory to save downloaded fastq files
`srcType`	type of transfer protocol, which should be "ftp" or "fasp".
`makeDirectory`	logical, TRUE or FALSE. If TRUE and baseDir does not exists, storedir will be created to save downloaded files, otherwise downloaded fastq files will be saved to current directory.
`method`	character vector of length 1, passed to the identically named argument of `download.file`.
`ascpCMD`	ascp main commands, which should be constructed by a user according to the actual installation of Aspera Connect in the system, with proper options to be used. Example commands: "ascp -QT -l 300m -i /usr/local/aspera/connect/etc/asperaweb_id_dsa.putty" (Linux) or "'/Applications/Aspera Connect.app/Contents/Resources/ascp' -QT -l 300m -i '/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.putty'" (Mac OS X). More about ascp please see the help ('ascp -h' in a shell).

Details

The function first gets ftp/fasp addresses of SRA fastq files using funcitn getFASTQinfo for a given list of input SRA accessions; then downloads the fastq files through ftp or fasp.

Warning

Downloading SRA fastq files through ftp over long distance could take long time and should consider using using 'fasp'.

Author(s)

Jack Zhu <zhujack@mail.nih.gov>

Examples

## Using the SRAmetadb demo database

	## Not run: 
	library(SRAdb)
	sra_dbname <- file.path(system.file('extdata', package='SRAdb'), 'SRAmetadb_demo.sqlite')	
	sra_con <- dbConnect( dbDriver("SQLite"), sra_dbname )
	
	## Download fastq files from EBI ENA  through ftp
	getFASTQfile( in_acc = c("SRR000648","SRR000657"), sra_con, destDir = getwd(), srcType = 'ftp', ascpCMD = NULL )
		
	## Download fastq files from EBI ENA  through fasp
	ascpCMD <- 'ascp -QT -l 300m -i /usr/local/aspera/connect/etc/asperaweb_id_dsa.putty'
	## common ascpCMD for a system with Mac OS X:
	#ascpCMD <- "'/Applications/Aspera Connect.app/Contents/Resources/ascp' -QT -l 300m -i '/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.putty'"	
	getFASTQfile( in_acc = c("SRR000648","SRR000657"), sra_con, srcType='fasp', ascpCMD=ascpCMD )
	
	dbDisconnect( sra_con )
	
## End(Not run)

## The actual SRAmetadb sqlite database can be downloaded using function: getSRAdbFile. Warning: the actual SRAmetadb sqlite database is pretty large (> 35GB as of May, 2018) after uncompression. So, downloading and uncompressing of the actual SRAmetadb sqlite could take quite a few minutes depending on your network bandwidth. Direct links for downloading the SRAmetadb sqlite database:  https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz

zhujack/SRAdb documentation built on Oct. 26, 2022, 7:32 a.m.