R: Get BOLD specimen + sequence data.

bold_seqspec {bold} | R Documentation

## Get BOLD specimen + sequence data.

### Description

Get BOLD specimen + sequence data.

### Usage

    bold_seqspec(taxon = NULL, ids = NULL, bin = NULL, container = NULL,
      institutions = NULL, researchers = NULL, geo = NULL, marker = NULL,
      response = FALSE, format = "tsv", sepfasta = 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. See Details.
`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.
`format` | (character) One of xml or tsv (default). tsv format gives back a data.frame object. xml gives back parsed xml as a
`sepfasta` | (logical) If `TRUE`, the fasta data is separated into a list with names matching the processid's from the data frame. Default: `FALSE`
`...` | Further args passed on to `HttpClient`, main purpose being curl debugging

### Value

Either a data.frame, parsed xml, a http response object, or a list with length two (a data.frame w/o nucleotide data, and a list with nucleotide data)

### Marker

Notes from BOLD on the `marker` param: "All markers for a specimen matching the search string will be returned. ie. A record with COI-5P and ITS will return sequence data for both markers even if only COI-5P was specified."

You will likely end up with data with markers that you did not request - just be sure to filter those out as needed.

### References

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

### Examples

    ## Not run:
    bold_seqspec(taxon='Osmia')
    bold_seqspec(taxon='Osmia', format='xml')
    bold_seqspec(taxon='Osmia', response=TRUE)
    res <- bold_seqspec(taxon='Osmia', sepfasta=TRUE)
    res$fasta[1:2]
    res$fasta['GBAH0293-06']

    # records that match a marker name
    res <- bold_seqspec(taxon="Melanogrammus aeglefinus", marker="COI-5P")

    # records that match a geographic locality
    res <- bold_seqspec(taxon="Melanogrammus aeglefinus", geo="Canada")

    ## curl debugging
    ### You can do many things, including get verbose output on the curl call,
    ### and set a timeout
    head(bold_seqspec(taxon='Osmia', verbose = TRUE))
    ## timeout
    # head(bold_seqspec(taxon='Osmia', timeout_ms = 1))

    ## End(Not run)

[Package bold version 0.5.0 Index]