bold (version 1.3.0)

bold_trace: Get BOLD trace files

Description

Get BOLD trace files

Usage

bold_trace(
  taxon = NULL,
  ids = NULL,
  bin = NULL,
  container = NULL,
  institutions = NULL,
  researchers = NULL,
  geo = NULL,
  marker = NULL,
  dest = NULL,
  overwrite = TRUE,
  progress = TRUE,
  ...
)
# S3 method for boldtrace
print(x, ...)
read_trace(x)
bold_read_trace(x)

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.

dest

(character) A directory to write the files to

overwrite

(logical) Overwrite existing directory and file?

progress

(logical) Print progress or not. NOT AVAILABLE FOR NOW. HOPEFULLY WILL RETURN SOON.

...

Further args passed on to verb-GET

x

(list or character) Either the boldtrace object returned from bold_trace or the path(s) of bold trace file(s).

References

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

Examples

if (FALSE) {
# Use a specific destination directory
bold_trace(taxon = "Bombus ignitus", geo = "Japan", dest = "~/mytarfiles")

# Another example
# bold_trace(ids='ACRJP618-11', dest="~/mytarfiles")
# bold_trace(ids=c('ACRJP618-11','ACRJP619-11'), dest="~/mytarfiles")

# read file in
x <- bold_trace(ids=c('ACRJP618-11','ACRJP619-11'), dest="~/mytarfiles")
(res <- read_trace(x$ab1[2]))
# read all files in
(res <- read_trace(x))

# The progress dialog is pretty verbose, so quiet=TRUE is a nice touch,
# but not by default
# Beware, this one take a while
# x <- bold_trace(taxon='Osmia', quiet=TRUE)

if (requireNamespace("sangerseqR", quietly = TRUE)) {
 library("sangerseqR")
 primarySeq(res)
 secondarySeq(res)
 head(traceMatrix(res))
}
}