getSRAinfo: Get SRA data file information from NCBI SRA

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

View source: R/getSRAinfo.R

Description

This function gets SRA .sra file information from NCBI SRA ftp site for a given list SRA accessions.

Usage

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getSRAinfo( in_acc, sra_con, sraType = 'sra' )

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

sraType

type of SRA data files, which should be 'sra' ('litesra' has phased out ).

Details

The function first gets ftp addressed of sra or sra-lite data files with function listSRAfile and then get file size and date from NCBI SRA ftp sites.

Value

A data.frame of ftp addresses of SRA data files, and file size and date along with input SRA accessions.

Author(s)

Jack Zhu <z[email protected]>

See Also

listSRAfile, getSRAfile

Examples

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if(file.exists('SRAmetadb.sqlite')) {

	library(SRAdb)
	sra_dbname <- 'SRAmetadb.sqlite'	
	sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
	
	## Get file size and date from NCBI ftp site for available fastq files associated with "SRS012041","SRS000290"
	# getSRAinfo (in_acc=c("SRS012041","SRS000290"), sra_con=sra_con, sraType='sra')

} 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.