getFASTQinfo: Get SRA fastq file information and associated meta data from...
In seandavi/SRAdb: A compilation of metadata from NCBI SRA and tools

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

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.

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

`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'.

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.

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. ).

Jack Zhu <zhujack@mail.nih.gov>

getFASTQfile, listSRAfile, getSRAfile

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")
}