SRAdb (version 1.30.0)

getSRAinfo: Get SRA data file information from NCBI SRA

Description

This function gets SRA .sra file information from NCBI SRA ftp site for a given list SRA accessions.

Usage

getSRAinfo( in_acc, sra_con, sraType = 'sra' )

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

sraType

type of SRA data files, which should be 'sra' ('litesra' has phased out ).

Value

A data.frame of ftp addresses of SRA data files, and file size and date along with input SRA accessions.

Details

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.

See Also

listSRAfile, getSRAfile

Examples

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='sra')

} else {
  	print(" use getSRAdbFile() to get a copy of the SRAmetadb.sqlite file  and then rerun the example")
}