geomedb (version 2.0.1)

prefetch: 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.

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.

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"

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)
# }