BAGS: Barcode, Audit & Grade System

<div style="border: 2px solid red; padding: 15px; background-color: #ffe6e6; font-size: 18px;"> <h1 style="color:red; text-align:center;">⚠️ Important Notice ⚠️</h1> <p> The BAGS output may be affected by the removal of the bold R package from the CRAN repository. While earlier versions are still available through the CRAN archive, the removal may impact accessibility and usability moving forward. BAGS was developed to work with the BOLD Systems API v4, and with the ongoing transition to API v5, its compatibility with future updates remains uncertain. <strong>Please be cautious when interpreting results and aware of potential limitations or inaccuracies.</strong>

BAGS continues to download current data from BOLD via the v4 API, including newly added records. However, grade assignment relies on static reference files that cannot be updated at this time. These files—last updated in July 2024—store the BIN-to-species mapping used to calculate the number of BINs per species name and the number of species names per BIN. As a result, any BIN reassignments or changes in species-BIN relationships after that date are not accounted for in the grading process.

When a species is assigned the grade "needs_update", it means BAGS detected at least one BIN that was not included in the current static reference files on GitHub. In such cases, while the sequence data are retrieved and included, the grading is based only on the outdated BIN-to-species mapping. Consequently, some grade assignments may show discrepancies when compared to the current BIN structure on BOLD.

🧭To address these limitations, we are currently testing an experimental version of BAGS available at:
https://tadeu-apps.shinyapps.io/bags4/ AND https://tadeu-apps.shinyapps.io/bags5/. This version may take longer to retrieve data, but grade assignment is done in real time, using up-to-date BIN-to-species information directly from the current BOLD API responses.
Therefore, the issues described above regarding outdated static files do not apply to this version.
If you try it out, we would greatly appreciate any feedback, bug reports, or suggestions to help improve it and eventually extend this version to the other available Shinyapps links, as well as the self-hosted (local) version.

</p> <p> </p> </div>

Available links for direct access to BAGS:

NOTE: the web links have limited capacity for the retrieval or large taxonomic groups, and they are limited to one user at a time. To run BAGS without limitations, host the application locally in your R environment

How to host BAGS locally in your R environment

Running BAGS from GitHub:

Download and install the most suited version of R for your operating system.
Optionally you can download and install RStudio.
Open RGui or Rstudio and run this line of code to install the necessary packages:

install.packages(c("data.table","plyr","httr","stringr","readr","fingerprint","dplyr","ggplot2","shiny","shinyWidgets","snakecase"))

The packages "bold", "seqRFLP", and "worms" have been removed from the CRAN repository. To install the package "bold" from the CRAN archive, run these lines of code:

install.packages("crul")
url <- "http://cran.r-project.org/src/contrib/Archive/bold/bold_1.3.0.tar.gz"
pkgFile <- "bold_1.3.0.tar.gz"
download.file(url = url, destfile = pkgFile)
install.packages(pkgs=pkgFile, type="source", repos=NULL)

To install the package "seqRFLP" from the CRAN archive, run these lines of code:

url <- "http://cran.r-project.org/src/contrib/Archive/seqRFLP/seqRFLP_1.0.1.tar.gz"
pkgFile <- "seqRFLP_1.0.1.tar.gz"
download.file(url = url, destfile = pkgFile)
install.packages(pkgs=pkgFile, type="source", repos=NULL)

To install the package "worms" from the CRAN archive, run these lines of code:

url <- "http://cran.r-project.org/src/contrib/Archive/worms/worms_0.2.2.tar.gz"
pkgFile <- "worms_0.2.2.tar.gz"
download.file(url = url, destfile = pkgFile)
install.packages(pkgs=pkgFile, type="source", repos=NULL)

Load the "shiny" package by running:

library(shiny)

Run the app from GitHub:

runGitHub("BAGS", "tadeu95")

Running BAGS by manually downloading the app file to your computer:

Download and install the most suited version of R for your operating system.
Optionally you can download and install RStudio.
Open RGui or Rstudio and install the necessary packages:

install.packages(c("data.table","stringr","readr","fingerprint","dplyr","ggplot2","shiny","shinyWidgets","snakecase"))
url <- "http://cran.r-project.org/src/contrib/Archive/bold/bold_1.3.0.tar.gz"
pkgFile <- "bold_1.3.0.tar.gz"
download.file(url = url, destfile = pkgFile)
install.packages(pkgs=pkgFile, type="source", repos=NULL)
url <- "http://cran.r-project.org/src/contrib/Archive/seqRFLP/seqRFLP_1.0.1.tar.gz"
pkgFile <- "seqRFLP_1.0.1.tar.gz"
download.file(url = url, destfile = pkgFile)
install.packages(pkgs=pkgFile, type="source", repos=NULL)
url <- "http://cran.r-project.org/src/contrib/Archive/worms/worms_0.2.2.tar.gz"
pkgFile <- "worms_0.2.2.tar.gz"
download.file(url = url, destfile = pkgFile)
install.packages(pkgs=pkgFile, type="source", repos=NULL)

Go to "File" on the top left corner, click "Open file" / "Open script" and choose the "app" file.
In the top right corner of the opened app script file, click "run app" if you're on RStudio. Another alternative is to run the script line by line using ctrl+ENTER for each chunk of code. If you're on RGui, select all the text in the script file (Ctrl+A) then click the right button of the mouse and choose "Run line or selection" (Ctrl+R).
After running the script, a window with the app will pop up, and you can click "open in browser" to run the app in your default browser if you're on RStudio. If you're on RGui, the app will automatically open in your default browser.

BAGS

Install / Use

README