bold_identify {bold}

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,
  db = c("COX1", "COX1_SPECIES", "COX1_SPECIES_PUBLIC", "COX1_L640bp"),
  response = FALSE,
  keepSeq = TRUE,
  ...
)

Arguments

sequences

(character) A vector or list of sequences to identify. Required. See Details.

db

(character) The database to match against, one of COX1 (default), COX1_SPECIES, COX1_SPECIES_PUBLIC, OR COX1_L640bp. 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.

keepSeq

(logical) If TRUE (default), returns each data.frame with an attribute 'sequence' containing sequence used to get those results.

...

Further args passed on to verb-GET, main purpose being curl debugging

Details

BOLD only allows one sequences per query. We internally lapply over the input values given to the sequences' parameter to search with one sequences per query. Remember this if you have a lot of sequences - you are doing a separate query for each one, so it can take a long time - if you run into errors let us know.

Value

A data.frame or list of (one per sequences) with the top specimen matches (up to 100) and their details. If the query fails, returns NULL. Each data.frame has the attributes sequence with the provided sequence to match (unless keepSeq is set to FALSE) and errors with the error message given from a failed request.

db parmeter options

• COX1 Every COI barcode record on BOLD with a minimum sequences 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 Every COI barcode record with a species level identification and a minimum sequences length of 500bp. This includes many species represented by only one or two specimens as well as all species with interim taxonomy. Note : Sometimes it does return matches that don't have a species level identification. Will be checking with BOLD.

• COX1_SPECIES_PUBLIC All published COI records from BOLD and GenBank with a minimum sequences length of 500bp. This library is a collection of records from the published projects section of BOLD.

• OR COX1_L640bp Subset of the Species library with a minimum sequences length of 640bp and containing both public and private records. This library is intended for short sequences identification as it provides maximum overlap with short reads from the barcode region of COI.

Named outputs

For a named output list, make sure to pass in a named list or vector to the sequences parameter. You can use names<- or setNames to set names on a list or vector of sequences.

References

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

See Also

bold_identify_parents

Examples

## Not run: 
seq <- sequences$seq1
res <- bold_identify(sequences=seq)
head(res[[1]])
head(bold_identify(sequences=seq, db='COX1_SPECIES')[[1]])

## End(Not run)