prefetch: Download data from NCBI Sequence Read Archive in .sra format...

In DIPnet/fimsR-access: Functions for Fetching 'GeOMe-db' Data

Download data from NCBI Sequence Read Archive in .sra format using FASP or HTTPS protocols

Description

'prefetch()' uses the SRAtoolkit command-line function 'prefetch' to download .sra files from all samples returned by a queryMetadata query of GEOME, when one of the entities queried was 'fastqMetadata'

Usage

prefetch(queryMetadata_object, sratoolkitPath = "",
  outputDirectory = ".", arguments = "-p 1", prefetchHelp = FALSE)

Arguments

queryMetadata_object	A list object returned from 'queryMetadata' where one of the entities queried was 'fastqMetadata'.
sratoolkitPath	String. A path to a local copy of sratoolkit. Only necessary if sratoolkit is not on your $PATH. Assumes executables are inside 'bin'.
outputDirectory	String. A path to the directory where you would like the files to be stored.
arguments	A string variable of arguments to be passed directly to 'prefetch'. Defaults to "-p 1" to show progress. Use prefetchHelp = TRUE to see a list of arguments.
prefetchHelp	Logical. prefetchHelp = T will show the help page for 'prefetch' and then quit.

Details

This function works best with SRAtoolkit functions of version 2.9.6 or greater. SRAtoolkit functions can (ideally) be in your $PATH, or you can supply a path to them using the sratoolkitPath argument.

It downloads files to the current working directory unless a different one is assigned through outputDirectory.

'prefetch' will automatically use the Fast and Secure Protocol (FASP) in the Aspera Connect package if the 'ascp' executable is in your $PATH. Otherwise it will use HTTPS.

You can alternatively pass the path to 'ascp' by using arguments="-a path/to/ascp"

Value

This function will not return anything within r. It simply downloads .sra files. It will print command line stdout to the console, and also provide a start and end time and amount of time elapsed during the download.

See Also

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc to download pre-compiled executables for sratoolkit or https://github.com/ncbi/sra-tools/wiki/Building-and-Installing-from-Source> to install from source

Use 'prefetch' in combination with fastqDump or fasterqDump to convert .sra files to .fastq.

Examples

## Not run: 
# Run a query of GEOME first
acaoli <- queryMetadata(
   entity = "fastqMetadata", 
   query = "genus = Acanthurus AND specificEpithet = olivaceus AND _exists_:bioSample",
   select=c("Event"))

#trim to 3 entries for expediency
acaoli$fastqMetadata<-acaoli$fastqMetadata[1:3,]
acaoli$Event<-acaoli$Event[1:3,]


prefetch(queryMetadata_object = acaoli)

fastqDump(queryMetadata_object = acaoli, filenames = "IDs", source = "local", cleanup = T)

## End(Not run)

DIPnet/fimsR-access documentation built on Nov. 12, 2022, 2:41 a.m.