| bold_seqspec {bold} | R Documentation |
Get BOLD specimen + sequence data.
bold_seqspec(taxon = NULL, ids = NULL, bin = NULL, container = NULL, institutions = NULL, researchers = NULL, geo = NULL, marker = NULL, response = FALSE, format = "tsv", sepfasta = FALSE, ...)
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 |
... |
Further args passed on to |
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)
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.
http://v4.boldsystems.org/index.php/resources/api?type=webservices
## 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)