getRepeatMasker: Repeat Masker Retrieval

Description

Main Repeat Masker output retrieval function for an organism of interest. By specifying the scientific name of an organism of interest the corresponding Repeat Masker file storing the genome of the organism of interest can be downloaded and stored locally. Repeat Masker files can be retrieved from several databases.

Usage

getRepeatMasker(
  db = "refseq",
  organism,
  reference = FALSE,
  skip_bacteria = TRUE,
  release = NULL,
  gunzip = FALSE,
  path = file.path("_ncbi_downloads", "repeatmasker"),
  mute_citation = FALSE
)

Value

File path to downloaded Repeat Masker output file.

Arguments

db

a character string specifying the database from which the genome shall be retrieved:

db = "refseq"
db = "genbank"

organism

a character string specifying the scientific name of the organism of interest, e.g. organism = "Homo sapiens".

reference

a logical value indicating whether or not a genome shall be downloaded if it isn't marked in the database as either a reference genome or a representative genome.

skip_bacteria

Due to its enormous dataset size (> 700MB as of July 2023), the bacterial summary file will not be loaded by default anymore. If users wish to gain insights for the bacterial kingdom they needs to actively specify skip_bacteria = FALSE. When skip_bacteria = FALSE is set then the bacterial summary file will be downloaded.

release

most recent database version is used. release = 75 would for human would give the stable GRCh37 release in ensembl. Value must be > 46, since ensembl did not structure their data if the standard format before that.

gunzip

a logical, indicating whether or not files should be unzipped.

path

a character string specifying the location (a folder) in which the corresponding file shall be stored. Default is path = file.path("_ncbi_downloads","repeatmasker").

mute_citation

logical value indicating whether citation message should be muted.

Author

Hajk-Georg Drost

Details

Internally this function loads the the overview.txt file from NCBI:

refseq: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/

genbank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/

and creates a directory '_ncbi_downloads/repeatmasker' to store the files of interest as fasta file for future processing. In case the corresponding fasta file already exists within the '_ncbi_downloads/repeatmasker' folder and is accessible within the workspace, no download process will be performed.

Examples

Run this code

if (FALSE) {

# download the Repeat Masker output file of Homo sapiens from refseq
# and store the corresponding genome file in '_ncbi_downloads/genomes'
file_path <- getRepeatMasker( db       = "refseq",
             organism = "Homo sapiens",
             path = file.path("_ncbi_downloads","repeatmasker"))

Hsap_repeatmasker <- read_rm(file_path)

}

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