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

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

View source: R/listSRAfile.R

Description

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

Usage

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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 <[email protected]>

See Also

getSRAfile

Examples

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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")
}

seandavi/SRAdb documentation built on Feb. 21, 2018, 5:21 a.m.