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Download records from BOLD

Source: R/download_bold.R
download_bold.Rd

This function searches for BOLD records corresponding to the species found in the argument `bold_tax`, i.e. the output from the function `get_bold_taxonomy`.

For a thorough explanation of the function usage and capabilities, see the 'Introduction to the barcodeMineR package' vignette: vignette("Introduction to the barcodeMineR package", package = "barcodeMineR")

Usage

download_bold(
  bold_tax,
  rate = 100,
  api_rate = NULL,
  ask = TRUE,
  prefix = NULL,
  filter = TRUE
)

Arguments

bold_tax

a data.frame, as returned from the get_bold_taxonomy function.

rate

`integer` The number of records to be downloaded at a time. It can be lowered for unstable internet connections. However, due to the structure of the bold package, it is not possible to download a specific number of records when a species is represented by more than `rate` records. This function only groups species whose sum of records is inferior to rate. Defaults to `100`.

api_rate

`integer` The API rate with which to iterate each separate request. Must be a number between 3 and 10 which will translate in a rate of `1 / api_rate` seconds.

ask

`logical` Should the function ask the user whether to filter the final output for taxonomic ranks. Default `TRUE`.

prefix

`character` A character string that will be used to create numbered custom ids for each record in ascending order. The prefix will compose the recordID field in the final object. Default to `NULL`, using the internal recordID generator that will use the accession number for NCBI records and the processID for BOLD records, avoiding duplicates by adding `_1`, `_2` etc.

filter

`logical` Whether to filter records retaining only those corresponding exactly to the taxa found in the taxonomy table `bold_tax` or include also those corresponding to children taxonomies. Default to `TRUE`.

Value

`data.frame` A refdb data frame, including the DNA sequence as a field.

See also

[download_ncbi()]

Examples

tax <- get_bold_taxonomy("Polymastia invaginata")

download_bold(tax, ask = FALSE)
#> # A tibble: 6 × 30
#>   recordID     markerCode DNA_seq phylum class order family genus species source
#>   <chr>        <chr>      <DNA>   <chr>  <chr> <chr> <chr>  <chr> <chr>   <chr> 
#> 1 GBMAA106-14  COI-5P     GACTCT… Porif… Demo… Poly… Polym… Poly… Polyma… BOLD  
#> 2 GBMAA150-14  COI-5P     GACTCT… Porif… Demo… Poly… Polym… Poly… Polyma… BOLD  
#> 3 GBMIN44241-… COI-5P     GACTCT… Porif… Demo… Poly… Polym… Poly… Polyma… BOLD  
#> 4 GBMIN44242-… COI-5P     GTATGT… Porif… Demo… Poly… Polym… Poly… Polyma… BOLD  
#> 5 GBMIN44243-… COI-5P     GTATGT… Porif… Demo… Poly… Polym… Poly… Polyma… BOLD  
#> 6 GBMIN44244-… COI-5P     GTATGT… Porif… Demo… Poly… Polym… Poly… Polyma… BOLD  
#> # ℹ 20 more variables: lat <dbl>, lon <dbl>, lengthGene <int>, sampleID <chr>,
#> #   QueryName <chr>, identified_by <lgl>, taxNotes <lgl>, db_xref <chr>,
#> #   sourceID <chr>, NCBI_ID <chr>, institutionStoring <lgl>,
#> #   collected_by <lgl>, collection_date <lgl>, altitude <lgl>, depth <lgl>,
#> #   country <chr>, directionPrimers <lgl>, lengthSource <int>,
#> #   PCR_primers <lgl>, note <chr>