getSRAdbFile: Download and unzip last version of SRAmetadb.sqlite.gz from...
In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

getSRAdbFile

R Documentation

Download and unzip last version of SRAmetadb.sqlite.gz from the server

Description

This function is the standard method for downloading and unzipping the most recent SRAmetadb SQLite file from the server.

Usage

getSRAdbFile(destdir = getwd(), destfile = "SRAmetadb.sqlite.gz",
             method)

Arguments

`destdir`	The destination directory of the downloaded file
`destfile`	The filename of the downloaded file. This filename should end in ".gz" as the unzipping assumes that is the case
`method`	Character vector of length 1, passed to the identically named argument of `download.file`.

Value

Prints some diagnostic information to the screen.

Returns the local filename for use later.

Author(s)

Jack Zhu <zhujack@mail.nih.gov>, Sean Davis <sdavis2@mail.nih.gov>

Examples

## the SRAmetadb demo database can be used to test
sra_dbname <- file.path(system.file('extdata', package='SRAdb'), 'SRAmetadb_demo.sqlite')	

## Not run: geometadbfile <- getSRAdbFile()
## 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 Oct. 26, 2022, 7:32 a.m.