Get BOLD trace files

Description

Get BOLD trace files

Usage

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bold_trace(taxon = NULL, ids = NULL, bin = NULL, container = NULL,
  institutions = NULL, researchers = NULL, geo = NULL, marker = NULL,
  dest = NULL, overwrite = TRUE, progress = TRUE, ...)

read_trace(x)

Arguments

taxon

(character) Returns all records containing matching taxa. Taxa includes the ranks of phylum, class, order, family, subfamily, genus, and species.

ids

(character) Returns all records containing matching IDs. IDs include Sample IDs, Process IDs, Museum IDs and Field IDs.

bin

(character) Returns all records contained in matching BINs. A BIN is defined by a Barcode Index Number URI.

container

(character) Returns all records contained in matching projects or datasets. Containers include project codes and dataset codes

institutions

(character) Returns all records stored in matching institutions. Institutions are the Specimen Storing Site.

researchers

(character) Returns all records containing matching researcher names. Researchers include collectors and specimen identifiers.

geo

(character) Returns all records collected in matching geographic sites. 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. Uses progress.

...

Futher args passed on to GET.

x

Object to print or read.

References

http://www.boldsystems.org/index.php/resources/api#trace

Examples

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## Not run: 
# Use a specific destination directory
bold_trace(taxon='Bombus', geo='Alaska', 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]))

# 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))
}

## End(Not run)