biomartr (version 0.9.0)

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,
  path = file.path("_ncbi_downloads", "repeatmasker"))

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.

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").

Value

File path to downloaded Repeat Masker output file.

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.

See Also

getProteome, getCDS, getGFF, getRNA, meta.retrieval, read_rm, getGenome

Examples

# NOT RUN {
# download the Repeat Masker output file of Arabidopsis thaliana from refseq
# and store the corresponding genome file in '_ncbi_downloads/genomes'
file_path <- getRepeatMasker( db       = "refseq", 
             organism = "Arabidopsis thaliana", 
             path = file.path("_ncbi_downloads","repeatmasker"))

Ath_repeatmasker <- read_rm(file_path)


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

Ath_repeatmasker <- read_rm(file_path)
# }
# NOT RUN {
# }