traits (version 0.2.0)

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, fuzzy = 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.

fuzzy

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

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

## Not run: 
# # 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")
# ## End(Not run)