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

Description Usage Arguments Details Value Author(s) References See Also Examples

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/).

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

`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.

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

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

Jack Zhu <zhujack@mail.nih.gov>

http://www.asperasoft.com/

ascpR, listSRAfile, getSRAfile, getFASTQinfo, getSRAinfo

if( file.exists('SRAmetadb.sqlite') ) {
	## Not run: 
	library(SRAdb)
	sra_dbname <- 'SRAmetadb.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)
} else {
	  print( "Use ascpSRAdbFile() to get a copy of the SRAmetadb.sqlite file  and then rerun the example" )
}