| getSRAinfo {SRAdb} | R Documentation |
This function gets SRA .sra or .lite.sra file information from NCBI SRA ftp site for a given list SRA accessions.
getSRAinfo( in_acc, sra_con, sraType = 'sra' )
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 |
sraType |
type of SRA data files, which should be either 'sra' or 'litesra'. |
The function first gets ftp addressed of sra or sra-lite data files with function listSRAfile and then get file size and date from NCBI SRA ftp sites.
A data.frame of ftp addresses of SRA data files, and file size and date along with input SRA accessions.
Jack Zhu <zhujack@mail.nih.gov>
if(file.exists('SRAmetadb.sqlite')) {
library(SRAdb)
sra_dbname <- 'SRAmetadb.sqlite'
sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
## Get file size and date from NCBI ftp site for available fastq files associated with "SRS012041","SRS000290"
# getSRAinfo (in_acc=c("SRS012041","SRS000290"), sra_con=sra_con, sraType='litesra')
} else {
print(" use getSRAdbFile() to get a copy of the SRAmetadb.sqlite file and then rerun the example")
}