README.Rmd

bold
====

```{r echo=FALSE}
knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  warning = FALSE,
  message = FALSE
)
```

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`bold` accesses BOLD barcode data.

The Barcode of Life Data Systems (BOLD) is designed to support the generation and application of DNA barcode data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench.

This package retrieves data from the BOLD database of barcode clusters, and allows for searching of over 1.7M public records using multiple search criteria including sequence data, specimen data, specimen *plus* sequence data, as well as trace files.

Documentation for the BOLD API: http://v4.boldsystems.org/index.php/api_home

See also the taxize book for more options for taxonomic workflows with BOLD: https://taxize.dev/

## Installation

__Installation instructions__

__Stable Version__

```{r eval=FALSE}
install.packages("bold")
```

__Development Version__

Install `sangerseqR` first (used in function `bold::bold_trace()` only)

For R < 3.5

```{r eval=FALSE}
source("http://bioconductor.org/biocLite.R")
biocLite("sangerseqR")
```

For R >= 3.5

```{r eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sangerseqR")
```

Then install `bold`

```{r eval=FALSE}
remotes::install_github("ropensci/bold")
```


## Usage
```{r}
library("bold")
```


### Search for sequence data only

By default you download `fasta` file, which is given back to you as a `data.frame`

```{r}
res <- bold_seq(taxon='Coelioxys')
head(res)
```

You can optionally get back the `crul` response object

```{r}
res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$response_headers
```

### Search for specimen data only

By default you download `tsv` format data, which is given back to you as a `data.frame`

```{r}
res <- bold_specimens(taxon='Osmia')
head(res[,1:8])
```

### Search for specimen plus sequence data

By default you download `tsv` format data, which is given back to you as a `data.frame`

```{r}
res <- bold_seqspec(taxon='Osmia', sepfasta=TRUE)
res$fasta[1:2]
```

Or you can index to a specific sequence like

```{r}
res$fasta['GBAH0293-06']
```

### Get trace files

This function downloads files to your machine - it does not load them into your R session - but prints out where the files are for your information.

```{r}
x <- bold_trace(ids = 'ACRJP618-11', progress = FALSE)
read_trace(x$ab1)
```

### Large data

Sometimes with `bold_seq()` you request a lot of data, which can cause problems due 
to BOLD's servers. 

An example is the taxonomic name _Arthropoda_. When you send a request like 
`bold_seq(taxon = "Arthropoda")` BOLD attempts to give you back sequences
for all records under _Arthropoda_. This, as you can imagine, is a lot of 
sequences. 


```{r}
library("taxize")
```

Using `taxize::downstream` get children of _Arthropoda_

```{r}
x <- downstream("Arthropoda", db = "ncbi", downto = "class")
nms <- x$Arthropoda$childtaxa_name
```

Optionally, check that the name exists in BOLD's data. Any that are not in 
BOLD will give back a row of NAs

```{r}
checks <- bold_tax_name(nms)
# all is good
checks[,1:5]
```

Then pass those names to `bold_seq()`. You could pass all names in at once,
but we're trying to avoid the large data request problem here, so run each 
one separately with `lapply` or a for loop like request. 

```{r eval = FALSE}
out <- lapply(nms, bold_seq)
```

## Citation

Get citation information for `bold` in R by running: `citation(package = 'bold')`

## Meta

* Please [report any issues or bugs](https://github.com/ropensci/bold/issues)
* License: MIT
* Get citation information for `bold` in R doing `citation(package = 'bold')`
* Please note that this project is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By participating in this project you agree to abide by its terms.