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 class '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).
Examples
if (FALSE) { # \dontrun{
# 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))
}
} # }