| getSRAfile {SRAdb} | R Documentation |
This function downloads sra and sra-lite data files associated with input SRA accessions from NCBI SRA or downloads fastq files from EBI ENA through ftp or fasp protocol.
getSRAfile( in_acc, sra_con, destDir = getwd(), fileType = 'litesra', srcType = 'ftp', makeDirectory = FALSE, method = 'curl', ascpCMD = NULL )
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 |
destDir |
destination directory to save downloaded files. |
fileType |
type of SRA data files, which should be "sra", "litesra" or "fastq". |
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 |
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). |
The function first gets ftp/fasp addresses of SRA data files with funcitn getSRAinfo for a given list of input SRA accessions; then downloads the SRA data files through ftp or fasp.
The sra or sra-lite data files are downloaded from NCBI SRA and the fastq files are downloaded from EBI ENA.
Downloading SRA data files through ftp over long distance could take long time and should consider using using 'fasp'.
Jack Zhu <zhujack@mail.nih.gov>
listSRAfile, getSRAinfo, getFASTQinfo, getFASTQfile
if( file.exists( 'SRAmetadb.sqlite' ) ) {
library(SRAdb)
sra_dbname <- 'SRAmetadb.sqlite'
sra_con <- dbConnect( dbDriver("SQLite"), sra_dbname )
## Not run:
## Download litesra files from NCBI SRA using ftp protocol:
getSRAfile( in_acc = c("SRR000648","SRR000657"), sra_con = sra_con, destDir = getwd(), fileType = 'litesra' )
## Convert NCBI SRA format (.lite.sra or .sra) data to fastq:
## Download SRA Toolkit: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software
## Run fastq-dump to
## system ("fastq-dump SRR000648.lite.sra")
## Download fastq files from EBI using ftp protocol:
getSRAfile( in_acc, sra_con, destDir = getwd(), fileType = 'fastq', srcType = 'ftp', makeDirectory = FALSE, method = 'curl', ascpCMD = NULL )
## Download fastq files from EBI ftp siteusing fasp protocol:
ascpCMD <- 'ascp -QT -l 300m -i /usr/local/aspera/connect/etc/asperaweb_id_dsa.putty'
getSRAfile( in_acc, sra_con, fileType = 'fastq', srcType = 'fasp', ascpCMD = ascpCMD )
## End(Not run)
dbDisconnect( sra_con )
} else {
print( "use getSRAdbFile() to get a copy of the SRAmetadb.sqlite file and then rerun the example" )
}