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) One or more taxonomic name. Optional.
- ids
(character|integer|numeric) One or more IDs. Optional. IDs include Sample IDs, Process IDs, Museum IDs and Field IDs.
- bin
(character) One or more Barcode Index Number URI. Optional.
- container
(character) One or more project codes or dataset codes. Optional.
- institutions
(character) One or more institution's name. Optional. Institutions are the Specimen Storing Site.
- researchers
(character) One or more researcher names. Optional. Include collectors and specimen identifiers.
- geo
(character) One or more geographic sites. Includes countries and province/states.
- marker
(character) Returns all records containing matching marker codes.
- response
(logical) Default : FALSE. If TRUE, returns the object from the Curl call. Useful for debugging and getting more detailed info on the API call.
- ...
Further args passed on to
crul::verb-GET, main purpose being curl debugging
Value
A data frame with each element as row and 5 columns for processid, identification, marker, accession, and sequence.
Note
If using the taxon parameter with another parameter, if the taxon isn't found in the public database, it will act as if no taxon was specified and try to return all the data for the other specified parameter. You can make sure that the taxon you're looking up has public records with bold_stats.
Large requests
Some requests can lead to errors. These often have to do with requesting
data for a rank that is quite high in the tree, such as an Order,
for example, Coleoptera. If your request is taking a long time,
it's likely that something will go wrong on the BOLD server side,
or we'll not be able to parse the result here in R because
R can only process strings of a certain length. bold
users have reported errors in which the resulting response from
BOLD is so large that we could not parse it.
A good strategy for when you want data for a high rank is to
do many separate requests for lower ranks within your target
rank. You can do this manually, or use the function
taxize::downstream to get all the names of a lower
rank within a target rank. There's an example in the README
(https://docs.ropensci.org/bold/#large-data)
If a request times out
This is likely because you're request was for a large number of sequences and the BOLD service timed out. You still should get some output, those sequences that were retrieved before the time out happened. As above, see the README (https://docs.ropensci.org/bold/#large-data) for an example of dealing with large data problems with this function.
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.
Examples
if (FALSE) { # \dontrun{
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]
} # }