bold (version 0.5.0)

bold_seqspec: 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))
# }