listSRAfile: List sra, sra-lite or fastq data file names associated with...

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

List sra, sra-lite or fastq data file names associated with input SRA accessions

Description

This function lists all sra, sra-lite or fastq data files associated with input SRA accessions

Usage

listSRAfile( in_acc, sra_con, fileType = 'sra', srcType = 'ftp' )

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
fileType	types of SRA data files, which should be 'sra' or 'fastq'. ('litesra' has phased out ).
srcType	type of transfer protocol, which should be "ftp" or "fasp".

Details

SRA fastq files are hosted at EBI ftp site (ftp://ftp.sra.ebi.ac.uk/vol1/fastq/) and .sra files are hosted at NCBI ftp site (ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/). 'litesra' has phased out.

Value

A data frame of matched SRA accessions and data file names with ftp or fasp addresses.

Author(s)

Jack Zhu <[e-mail]>

See Also

getSRAfile

Examples

## 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)

	## 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)

## 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 Dec. 6, 2024, 2:15 a.m.