bold (version 0.3.0)

bold_identify: Search for matches to sequences against the BOLD COI database.

Description

Search for matches to sequences against the BOLD COI database.

Usage

bold_identify(sequences = NULL, db = "COX1", response = FALSE, ...)

Arguments

sequences

(character) Returns all records containing matching marker codes.

db

(character) The database to match against, one of COX1, COX1_SPECIES, COX1_SPECIES_PUBLIC, OR COX1_L604bp. See Details for more information.

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 httr::GET, main purpose being curl debugging

Value

• A data.frame with details for each specimen matched.

Details

Detailed description of options for the db parmeter:

• COX1 Every COI barcode record with a species level identification and a minimum sequence length of 500bp. This includes many species represented by only one or two specimens as well as all species with interim taxonomy.
• COX1_SPECIES Every COI barcode record on BOLD with a minimum sequence length of 500bp (warning: unvalidated library and includes records without species level identification). This includes many species represented by only one or two specimens as well as all species with interim taxonomy. This search only returns a list of the nearest matches and does not provide a probability of placement to a taxon.
• COX1_SPECIES_PUBLIC All published COI records from BOLD and GenBank with a minimum sequence length of 500bp. This library is a collection of records from the published projects section of BOLD.
• OR COX1_L604bp Subset of the Species library with a minimum sequence length of 640bp and containing both public and private records. This library is intended for short sequence identification as it provides maximum overlap with short reads from the barcode region of COI.

References

http://www.boldsystems.org/index.php/resources/api?type=idengine

Examples

seq <- sequences$seq1
head(bold_identify(sequences=seq)[[1]])
head(bold_identify(sequences=seq, db='COX1_SPECIES')[[1]])
bold_identify(sequences=seq, response=TRUE)

# Multiple sequences
out <- bold_identify(sequences=c(sequences$seq2, sequences$seq3), db='COX1')
lapply(out, head)

# curl debugging
library('httr')
bold_identify(sequences=seq, response=TRUE, config=verbose())[[1]]