bold (version 0.3.0)

bold_seq: Search BOLD for sequences.

Description

Get sequences for a taxonomic name, id, bin, container, institution, researcher, geographic place, or gene.

Usage

bold_seq(taxon = NULL, ids = NULL, bin = NULL, container = NULL,
  institutions = NULL, researchers = NULL, geo = NULL, marker = NULL,
  response = FALSE, ...)

Arguments

taxon

(character) Returns all records containing matching taxa. Taxa includes the ranks of phylum, class, order, family, subfamily, genus, and species.

ids

(character) Returns all records containing matching IDs. IDs include Sample IDs, Process IDs, Museum IDs and Field IDs.

bin

(character) Returns all records contained in matching BINs. A BIN is defined by a Barcode Index Number URI.

container

(character) Returns all records contained in matching projects or datasets. Containers include project codes and dataset codes

institutions

(character) Returns all records stored in matching institutions. Institutions are the Specimen Storing Site.

researchers

(character) Returns all records containing matching researcher names. Researchers include collectors and specimen identifiers.

geo

(character) Returns all records collected in matching geographic sites. Geographic sites includes countries and province/states.

marker

(character) Returns all records containing matching marker codes.

response

(logical) Note that response is the object that returns from the Curl call, useful for debugging, and getting detailed info on the API call.

...

Further args passed on to httr::GET, main purpose being curl debugging

Value

• A list with each element of length 4 with slots for id, name, gene, and sequence.

References

http://www.boldsystems.org/index.php/resources/api#sequenceParameters

Examples

bold_seq(taxon='Coelioxys')
bold_seq(taxon='Aglae')
bold_seq(taxon=c('Coelioxys','Osmia'))
bold_seq(ids='ACRJP618-11')
bold_seq(ids=c('ACRJP618-11','ACRJP619-11'))
bold_seq(bin='BOLD:AAA5125')
bold_seq(container='ACRJP')
bold_seq(researchers='Thibaud Decaens')
bold_seq(geo='Ireland')
bold_seq(geo=c('Ireland','Denmark'))

# Return the httr response object for detailed Curl call response details
res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$url
res$status_code
res$headers

## curl debugging
### You can do many things, including get verbose output on the curl call, and set a timeout
library("httr")
bold_seq(taxon='Coelioxys', config=verbose())[1:2]
# bold_seqspec(taxon='Coelioxys', config=timeout(0.1))