| listSRAfile {SRAdb} | R Documentation |
This function lists all sra, sra-lite or fastq data files associated with input SRA accessions
listSRAfile( in_acc, sra_con, fileType = 'sra', srcType = 'ftp' )
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 |
fileType |
types of SRA data files, which should be 'sra', 'litesra' or 'fastq'. |
srcType |
type of transfer protocol, which should be "ftp" or "fasp". |
SRA fastq files are hosted at EBI ftp site (ftp://ftp.sra.ebi.ac.uk/vol1/fastq/) and .sra or .lite.sra files are hosted at NCBI ftp site (ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/). Note: NCBI SRA is phasing out 'litesra' files and currently 'litesra' ftp addresses are pointing to the 'sra' files.
A data frame of matched SRA accessions and data file names with ftp or fasp addresses.
Jack Zhu <zhujack@mail.nih.gov>
if( file.exists('SRAmetadb.sqlite') ) {
## Not run:
library(SRAdb)
sra_dbname <- 'SRAmetadb.sqlite'
sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
## List ftp or fasp addresses of sra files associated with "SRX000122"
listSRAfile (in_acc = c("SRX000122"), sra_con = sra_con, fileType = 'sra')
listSRAfile (in_acc = c("SRX000122"), sra_con = sra_con, fileType = 'sra', srcType='fasp')
## End(Not run)
} else {
print("use getSRAdbFile() to get a copy of the SRAmetadb.sqlite file and then rerun the example")
}