biomartr (version 0.9.0)

getAssemblyStats: Genome Assembly Stats Retrieval

Description

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

Usage

getAssemblyStats(db = "refseq", organism, reference = FALSE,
  type = "download", path = file.path("_ncbi_downloads",
  "genomeassembly_stats"))

Arguments

db

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

• db = "refseq"

• db = "genbank"

• db = "ensembl"

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.

type

shall only the file be retrieved (default) type = "download" or should the corresponding file be downloaded and subsequently be imported type = "import".

path

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

Value

File path to downloaded genome assembly stats 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/

to retrieve available scientific names of organisms and creates a directory '_ncbi_downloads/genomeassembly_stats' to store the Genome Assembly Stats of interest as text file for future processing. In case the corresponding fasta file already exists within the '_ncbi_downloads/genomeassembly_stats' folder and is accessible within the workspace, no download process will be performed.

An example genome assembly stats file can be found here: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/ GCF_000001405.36_GRCh38.p10/GCF_000001405.36_GRCh38.p10_assembly_stats.txt.

See Also

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

Examples

# NOT RUN {
# download the genome assembly stats file of Saccharomyces cerevisiae
# from NCBI RefSeq
# and store the corresponding genome file in 
# '_ncbi_downloads/genomeassembly_stats'
file_path <- getAssemblyStats( db = "refseq", 
                 organism = "Saccharomyces cerevisiae", 
                 path = file.path("_ncbi_downloads","genomeassembly_stats"))
# import the raw file as it is downloaded
Scerevisiae.stats <- read_assemblystats(file_path, type = "raw")

# download the genome assembly stats file of Saccharomyces cerevisiae
# from NCBI RefSeq 
# and import overall statistics of the genome assembly
Scerevisiae.stats.import <- getAssemblyStats( db = "refseq", 
                 organism = "Saccharomyces cerevisiae",
                 type = "import", 
                 path = file.path("_ncbi_downloads","genomeassembly_stats"))
# }
# NOT RUN {
# }