getFASTQinfo: Get SRA fastq file information and associated meta data from...

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

View source: R/getFASTQinfo.R

Description

This function gets SRA fastq file information and essential associated meta data from EBI ENA web site ( http://www.ebi.ac.uk/ena/data/view/reports/sra/fastq_files/ ) for SRA accessions given.

Usage

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getFASTQinfo( in_acc, sra_con, srcType = 'ftp' )

Arguments

in_acc

character vector of SRA accessions that could be be in one or more SRA sata types: study, sample, experiment and/or run.

sra_con

Connection to the SRAmetadb SQLite database

srcType

option for listing either 'ftp' or 'fasp' addresses. The default is 'ftp'.

Details

EBI ENA web site ( http://www.ebi.ac.uk/ena/data/view/reports/sra/fastq_files/ ) is the souce for parsing infromation from, which is updated and verified daily. Ftp or fasp addresses got from this funciton can be used in either getFASTQfile or getSRAfile to download the files.

Value

A data.frame of ftp/fasp inftomation ( addresses, file size, read number, etc) and associated meta data ( study, sample, experiment, run, organism, instrument.platform, instrument.model, library.name, library.layout, library.source, library.selection, run.read.count, run.base.count, etc. ).

Author(s)

Jack Zhu <[email protected]>

See Also

getFASTQfile, listSRAfile, 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)	
	getFASTQinfo( in_acc = c("SRR000648","SRR000657"), sra_con, srcType = 'ftp' )
	getFASTQinfo( in_acc = c("SRR000648","SRR000657"), sra_con, 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.