getSRAdbFile: Download and unzip last version of SRAmetadb.sqlite.gz from...

In SRAdb: A compilation of metadata from NCBI SRA and tools

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 <[e-mail]>, Sean Davis <[e-mail]>

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

Example output

Loading required package: RSQLite
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: RCurl
Loading required package: bitops
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

SRAdb documentation built on Nov. 8, 2020, 6:49 p.m.