getSRAinfo: Get SRA data file information from NCBI SRA

In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

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 ).

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.

Value

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

Author(s)

Jack Zhu <[e-mail]>

See Also

listSRAfile, getSRAfile

Examples

## Using the SRAmetadb demo database

	library(SRAdb)
	sra_dbname <- file.path(system.file('extdata', package='SRAdb'), 'SRAmetadb_demo.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')

## 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

zhujack/SRAdb documentation built on Oct. 26, 2022, 7:32 a.m.