| bold_trace {bold} | R Documentation |
Get BOLD trace files
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)
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. NOT AVAILABLE FOR NOW. HOPEFULLY WILL RETURN SOON. |
... |
Further args passed on to |
x |
Object to print or read. |
http://v4.boldsystems.org/index.php/resources/api?type=webservices
## 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)