GFF retrieval of multiple speciesSource:
Main GFF retrieval function for a set of organism of interest. By specifying the scientific names of the organisms of interest the corresponding fasta-files storing the GFF of the organisms of interest will be downloaded and stored locally. GFF files can be retrieved from several databases.
getGFFSet( db = "refseq", organisms, reference = FALSE, release = NULL, skip_bacteria = TRUE, gunzip = TRUE, remove_annotation_outliers = FALSE, update = FALSE, format = "gff3", path = "set_GFF", mute_citation = FALSE )
a character string specifying the database from which the genome shall be retrieved:
db = "refseq"
db = "genbank"
db = "ensembl"
a character vector storing the names of the organisms than shall be retrieved. There are three available options to characterize an organism:
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.
a numeric, the database release version of ENSEMBL (
db = "ensembl"). Default is
release = NULLmeaning that the most recent database version is used.
release = 75would 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.
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 = FALSEis set then the bacterial summary file will be downloaded.
a logical, indicating whether or not files should be unzipped.
shall outlier lines be removed from the input
annotation_file? If yes, then the initial
annotation_filewill be overwritten and the removed outlier lines will be stored at
tempdirfor further exploration.
logical, default FALSE. Updated backend cached files needed. Usually keep this false, to make ut run much faster. Only set to TRUE, if you believe you cache is outdated (Species only exist in newest release etc)
"gff3", alternative "gtf" for ensembl.
character, default location is paste0("set_", toupper(set_type))
logical, default FALSE, indicating whether citation message should be muted.
File path to downloaded genomes (names are identifiers: 'new' (file was downloaded now), 'old' files did already exist)
Internally this function loads the the overview.txt file from NCBI:
and creates a directory 'set_CDSs' to store the CDSs of interest as fasta files for future processing. In case the corresponding fasta file already exists within the 'set_CDSs' folder and is accessible within the workspace, no download process will be performed.