traits (version 0.1.0)

ncbi_searcher: Search for gene sequences available for taxa from NCBI.

Description

Search for gene sequences available for taxa from NCBI.

Usage

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

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.

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. (http://www.ncbi.nlm.nih.gov/books/NBK383

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

verbose

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

Value

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

See Also

ncbi_getbyid, ncbi_getbyname

Examples

# 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]")