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

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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".

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.

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

Jack Zhu <zhujack@mail.nih.gov>

getSRAfile

if( file.exists('SRAmetadb.sqlite') ) {
	## Not run: 
	library(SRAdb)
	sra_dbname <- 'SRAmetadb.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)
} else {
	print("use getSRAdbFile() to get a copy of the SRAmetadb.sqlite file  and then rerun the example")
}