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Search for gene sequences available for taxa from NCBI.

Source: R/ncbi_searcher.R
ncbi_searcher.Rd

Search for gene sequences available for taxa from NCBI.

Usage

ncbi_searcher(
  taxa = NULL,
  id = NULL,
  seqrange = "1:3000",
  getrelated = FALSE,
  fuzzy = FALSE,
  limit = 500,
  entrez_query = NULL,
  hypothetical = FALSE,
  verbose = TRUE,
  sleep = 0L
)

Arguments

taxa

(character) Scientific name to search for.

id

(character) Taxonomic id to search for. Not compatible with argument taxa.

seqrange

(character) Sequence range, as e.g., "1:1000". This is the range of sequence lengths to search for. So "1:1000" means search for sequences from 1 to 1000 characters in length.

getrelated

(logical) If TRUE, gets the longest sequences of a species in the same genus as the one searched for. If FALSE, returns nothing if no match found.

fuzzy

(logical) Whether to do fuzzy taxonomic ID search or exact search. If TRUE, we use xXarbitraryXx[porgn:__txid<ID>], but if FALSE, we use txid<ID>. Default: FALSE

limit

(numeric) Number of sequences to search for and return. Max of 10,000. If you search for 6000 records, and only 5000 are found, you will of course only get 5000 back.

entrez_query

(character; length 1) An Entrez-format query to filter results with. This is useful to search for sequences with specific characteristics. The format is the same as the one used to seach genbank. (https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options)

hypothetical

(logical; length 1) If FALSE, an attempt will be made to not return hypothetical or predicted sequences judging from accession number prefixs (XM and XR). This can result in less than the limit being returned even if there are more sequences available, since this filtering is done after searching NCBI.

verbose

(logical) If TRUE (default), informative messages printed.

sleep

(integer) number of seconds to sleep before each HTTP request. use if running to 429 Too Many Requests errors from NCBI. default: 0 (no sleep)

Value

data.frame of results if a single input is given. A list of data.frames if multiple inputs are given.

Authentication

NCBI rate limits requests. If you set an API key you have a higher rate limit. Set your API key like Sys.setenv(ENTREZ_KEY="yourkey") or you can use ?rentrez::set_entrez_key. set verbose curl output (crul::set_verbose()) to make sure your api key is being sent in the requests

See also

ncbi_byid, ncbi_byname

Author

Scott Chamberlain, Zachary Foster zacharyfoster1989@gmail.com

Examples

if (FALSE) { # \dontrun{
# A single species
out <- ncbi_searcher(taxa="Umbra limi", seqrange = "1:2000")
# Get the same species information using a taxonomy id
out <- ncbi_searcher(id = "75935", seqrange = "1:2000")
# If the taxon name is unique, using the taxon name and id are equivalent
all(ncbi_searcher(id = "75935") ==  ncbi_searcher(taxa="Umbra limi"))
# If the taxon name is not unique, use taxon id
#  "266948" is the uid for the butterfly genus, but there is also a genus
#  of orchids with the
#  same name
nrow(ncbi_searcher(id = "266948")) ==  nrow(ncbi_searcher(taxa="Satyrium"))
# get list of genes available, removing non-unique
unique(out$gene_desc)
# does the string 'RAG1' exist in any of the gene names
out[grep("RAG1", out$gene_desc, ignore.case=TRUE),]

# A single species without records in NCBI
out <- ncbi_searcher(taxa="Sequoia wellingtonia", seqrange="1:2000",
  getrelated=TRUE)

# Many species, can run in parallel or not using plyr
species <- c("Salvelinus alpinus","Ictalurus nebulosus","Carassius auratus")
out2 <- ncbi_searcher(taxa=species, seqrange = "1:2000")
lapply(out2, head)
library("plyr")
out2df <- ldply(out2) # make data.frame of all
unique(out2df$gene_desc) # get list of genes available, removing non-unique
out2df[grep("12S", out2df$gene_desc, ignore.case=TRUE), ]

# Using the getrelated and entrez_query options
ncbi_searcher(taxa = "Olpidiopsidales", limit = 5, getrelated = TRUE,
            entrez_query = "18S[title] AND 28S[title]")

# get refseqs
one <- ncbi_searcher(taxa = "Salmonella enterica",
  entrez_query="srcdb_refseq[PROP]")
two <- ncbi_searcher(taxa = "Salmonella enterica")
} # }