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

getFASTQinfo

R Documentation

Get SRA fastq file information and associated meta data from EBI ENA

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

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 <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)	
	getFASTQinfo( in_acc = c("SRR000648","SRR000657"), sra_con, srcType = 'ftp' )
	getFASTQinfo( in_acc = c("SRR000648","SRR000657"), sra_con, 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 Dec. 6, 2024, 2:15 a.m.