ascpSRA: Fasp SRA data file downloading using the ascp command line...
In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

ascpSRA

R Documentation

Fasp SRA data file downloading using the ascp command line program

Description

This function downloads SRA data files (fastq, sra ) by fasp protocol using Aspera's ascp command line program, which is included in Aspera Connect software (http://www.asperasoft.com/).

Usage

ascpSRA ( in_acc, sra_con, ascpCMD, fileType = 'sra', destDir = getwd() )

Arguments

`in_acc`	character vector of SRA accessions, which should be in same SRA data type, either submission, study, sample, experiment or run.
`sra_con`	connection to the SRAmetadb SQLite database.
`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).
`fileType`	type of SRA data files, which should be "sra", or "fastq" ('litesra' has phased out ).
`destDir`	destination directory to save downloaded files.

Details

This function will get fasp file sources first using funciton listSRAfile and then download data files using function ascpR.

Value

A data.frame of all matched SRA accessions and ftp or fasp file addresses.

Author(s)

Jack Zhu <zhujack@mail.nih.gov>

References

http://www.asperasoft.com/

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)
	in_acc <- c("SRR000648","SRR000657")
	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'"
	
	sraFiles <- ascpSRA( in_acc, sra_con, ascpCMD, fileType = 'sra', destDir=getwd() )
	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.