searchGB: Query the NCBI GenBank database.
In shaunpwilkinson/insect: Informatic Sequence Classification Trees

Description Usage Arguments Details Value Author(s) References See Also Examples

searchGB queries GenBank using the Entrez search utilities, and downloads the matching sequences and/or their accession numbers. A vector of accession numbers can be passed in lieu of a query, in which case the function downloads the matching sequences from GenBank. Internet connectivity is required.

searchGB(
  query = NULL,
  accession = NULL,
  sequences = TRUE,
  bin = TRUE,
  db = "nucleotide",
  taxIDs = TRUE,
  prompt = TRUE,
  contact = NULL,
  quiet = FALSE
)

`query`	an Entrez search query. For help compiling Entrez queries see https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options and https://www.ncbi.nlm.nih.gov/books/NBK49540/.
`accession`	an optional vector of GenBank accession numbers to be input in place of a search query. If both query and accession arguments are provided the function returns an error. Currently, a maximum of 200 accession numbers can be processed at a time.
`sequences`	logical. Should the sequences be returned or only the GenBank accession numbers? Note that taxon IDs are not returned if `sequences` is set to FALSE.
`bin`	logical indicating whether the returned sequences should be in raw-byte format ("DNAbin" or "AAbin" object type) or as a vector of named character strings. Defaults to TRUE.
`db`	the NCBI database from which to download the sequences and/or accession names. Accepted options are "nucleotide" (default) and "protein".
`taxIDs`	logical indicating whether the NCBI taxon ID numbers should be appended to the names of the output object (delimited by a "\|" character). Defaults to TRUE.
`prompt`	logical indicating whether to check with the user before downloading sequences.
`contact`	an optional character string with the users email address. This is added to the E-utilities URL and may be used by NCBI to contact the user if the application causes unintended issues.
`quiet`	logical indicating whether the progress should be printed to the console.

This function uses the Entrez e-utilities API to search and download sequences from GenBank. Occasionally users may encounter an unknown non-reproducible error and appears to be related to database records being updated in GenBank. This can generally be remedied by re-running the function. If problems persist please feel free to raise an issue on the package bug-reports page at <http://github.com/shaunpwilkinson/insect/issues>.

a list of sequences as either a DNAbin or AAbin object (depending on "db"), or a named vector of character strings (if bin = FALSE).

Shaun Wilkinson

NCBI Resource Coordinators (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 41 (Database issue): D8–D20.

read.GenBank (ape) for an alternative means of downloading DNA sequences from GenBank using accession numbers.

  ## Query the GenBank database for Eukaryote mitochondrial 16S DNA sequences
  ## between 100 and 300 base pairs in length that were modified between
  ## the years 1999 and 2000.
  
    query <- "Eukaryota[ORGN]+AND+16S[TITL]+AND+100:300[SLEN]+AND+1999:2000[MDAT]"
    x <- searchGB(query, prompt = FALSE)