getFile: Download any MGnify files, also including processed reads and...

In beadyallen/MGnifyR: R interface to EBI MGnify metagenomics resource

Download any MGnify files, also including processed reads and identified protein sequences

Description

Download any MGnify files, also including processed reads and identified protein sequences

Listing files available for download

Usage

getFile(x, ...)

searchFile(x, ...)

## S4 method for signature 'MgnifyClient'
getFile(x, url, file = NULL, read.func = NULL, ...)

## S4 method for signature 'MgnifyClient'
searchFile(
  x,
  accession,
  type = c("studies", "samples", "analyses", "assemblies", "genomes", "run"),
  ...
)

Arguments

x	A MgnifyClient object.
...	Additional arguments; not used currently.
url	A single character value specifying the url address of the file we wish to download.
file	A single character value or NULL specifying an optional local filename to use for saving the file. If NULL, MGNify local cache settings will be used. If the file is intended to be processed in a separate program, it may be sensible to provide a meaningful file, rather than having to hunt through the cache folders. If file is NULL and useCache(client) is FALSE, the read.func parameter must be supplied or the file will be downloaded and then deleted. (By default: file = NULL)
read.func	A function specifying an optional function to process the downloaded file and return the results, rather than relying on post processing. The primary use-case for this parameter is when local disk space is limited and downloaded files can be quickly processed and discarded. The function should take a single parameter, the downloaded filename, and may return any valid R object. (By default: read.func = NULL)
accession	A single character value or a vector of character values specifying accession IDs to return results for.
type	A single character value specifying the type of objects to query. Must be one of the following options: analysis, samples, studies, assembly, genome or run. (By default: type = "samples")

Details

getFile is a convenient wrapper round generic the URL downloading functionality in R, taking care of things like local caching and authentication.

searchFile() function is a wrapper function allowing easy enumeration of downloads available for a given accession IDs. Returns a single data.frame containing all available downloads and associated metadata, including the url location and description. This can then be filtered to extract the urls of interest, before actually retrieving the files using getFile()

Value

For getFile(), either the local filename of the downloaded file, be it either the location in the MGNifyR cache or file. If read.func is used, its result will be returned.

For searchFile() data.frame containing all discovered downloads. If multiple accessions are queried, the accessions column may to filter the results - since rownames are not set (and wouldn't make sense as each query will return multiple items)

Examples

# Make a client object
mg <- MgnifyClient(useCache = FALSE)

# Create a vector of accession ids - these happen to be \code{analysis}
# accessions
accession_vect <- c("MGYA00563876", "MGYA00563877")
downloads <- searchFile(mg, accession_vect, "analyses")

# Filter to find the urls of 16S encoding sequences
url_list <- downloads[
    downloads$attributes.description.label == "Contigs encoding SSU rRNA",
    "download_url"]

# Example 1:
# Download the first file
supplied_filename <- getFile(
    mg, url_list[[1]], file="SSU_file.fasta.gz")

## Not run: 
# Example 2:
# Just use local caching
cached_filename <- getFile(mg, url_list[[2]])

# Example 3:
# Using read.func to open the reads with readDNAStringSet from
# \code{biostrings}. Without retaining on disk
dna_seqs <- getFile(
    mg, url_list[[3]], read.func = readDNAStringSet)

## End(Not run)

# Make a client object
mg <- MgnifyClient(useCache = TRUE)
# Create a vector of accession ids - these happen to be \code{analysis}
# accessions
accession_vect <- c(
    "MGYA00563876", "MGYA00563877", "MGYA00563878",
    "MGYA00563879", "MGYA00563880" )
downloads <- searchFile(mg, accession_vect, "analyses")

beadyallen/MGnifyR documentation built on Dec. 3, 2024, 8:21 a.m.