listSRAfile: List sra, sra-lite or fastq data file names associated with...
In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

listSRAfile

R Documentation

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 <zhujack@mail.nih.gov>

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 Oct. 26, 2022, 7:32 a.m.