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Genome Assembly Stats Retrieval

Source: R/getAssemblyStats.R
getAssemblyStats.Rd

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,
  skip_bacteria = TRUE,
  release = NULL,
  type = "download",
  path = file.path("_ncbi_downloads", "genomeassembly_stats"),
  mute_citation = FALSE
)

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.

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.

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").

mute_citation

logical value indicating whether citation message should be muted.

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, getCollection, meta.retrieval, read_assemblystats

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# 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"))
} # }