getFASTQfile | R Documentation |
This function downloads SRA fastq data files through ftp or fasp from EBI ENA site for a given list of SRA accessions.
getFASTQfile( in_acc, sra_con, destDir = getwd(), srcType = 'ftp', makeDirectory = FALSE, method = 'curl', ascpCMD = NULL)
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 |
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 fastq files using funcitn getFASTQinfo
for a given list of input SRA accessions; then downloads the fastq files through ftp or fasp.
Downloading SRA fastq files through ftp over long distance could take long time and should consider using using 'fasp'.
Jack Zhu <zhujack@mail.nih.gov>
getFASTQinfo
, getSRAfile
, ascpR
## 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
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