ascpSRA: Fasp SRA data file downloading using the ascp command line...

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

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

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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/

See Also

ascpR, listSRAfile, getSRAfile, getFASTQinfo, getSRAinfo

Examples

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## 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

SRAdb documentation built on April 29, 2020, 5:22 a.m.