R: Search BOLD for sequences.

bold_seq {bold} | R Documentation

## 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 `HttpClient`, main purpose being curl debugging

### Value

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

### References

http://v4.boldsystems.org/index.php/resources/api?type=webservices

### Examples

    ## Not run:
    res <- 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 http response object for detailed Curl call response details
    res <- bold_seq(taxon='Coelioxys', response=TRUE)
    res$url
    res$status_code
    res$response_headers

    ## curl debugging
    ### You can do many things, including get verbose output on the curl
    ### call, and set a timeout
    bold_seq(taxon='Coelioxys', verbose = TRUE)[1:2]
    # bold_seqspec(taxon='Coelioxys', timeout_ms = 10)

    ## End(Not run)

[Package bold version 0.5.0 Index]