j9chan/buddysuite

Do fun stuff with biological data files. Seriously, biological data is fun stuff :)

Do fun stuff with biological data files. Seriously, biological data is fun stuff :)

___ ## Description The BuddySuite modules are designed to be 'one-stop-shop' command line tools for common biological data file manipulations.

SeqBuddy is the most mature BuddySuite tool, although AlignBuddy and PhyloBuddy are also functional with a more limited number of commands. DatabaseBuddy is a very different project, existing mostly as a 'live shell' for downloading sequences from GenBank, ENSEMBL, and UniProt.

Being pure Python, the BuddySuite should be cross platform. Development and testing have been done on Linux and Mac OS X, however, so it is unclear how well the suite will work within Windows.

Installation

Installation should be extremely easy on Mac and Linux using the graphical installer (Windows users must install the development version, see below).

Click here to download the graphical installer and run it from the command line

$: cd /path/to/download/folder
$: chmod +x BuddySuite_installer.py
$: ./BuddySuite_installer.py

By default, the installer will create short-form symbolic links for the main tools in your system $PATH ('sb' for SeqBuddy, 'alb' for AlignBuddy, 'pb' for PhyloBuddy, and 'db' for DatabaseBuddy), so they can be accessed quickly (examples in the wiki use these short forms). The full names of each tool will also be added to $PATH. If working outside the context of a graphical OS (on a cluster, for example), the installer will run in command-line mode (also accessible with the -cmd flag on graphical systems, if you prefer that).

The BuddySuite installer will only bundle stable release versions of the BuddySuite. If bugs are found they will be hot-fixed, but the expected behavior will not be changed once the release is finalized. Likewise, new features added to the development versions will not become available in the installer until the next release. Versions of each tool or the installer can be displayed using the -v flag.

Dependencies

This project has been written in Python3 and is not backwards compatible with Python2. If Python3 is not currently installed on your system, I highly recommend using the free Anaconda manager from Continuum Analytics (if you experience any difficulty, click here). Alternatively, the software can be downloaded directly from the Python Software Foundation.

AlignBuddy and PhyloBuddy can be used to launch a number of third party alignment and tree building programs, but installation of these optional programs is up to you. For example, if you wish to use PhyloBuddy to build a phylogenetic tree with RAxML, you will first need to get RAxML into your system PATH.

All other dependencies come prepackaged with the installer, so you only need to worry about the following if you are using the unstable workshop version of BuddySuite.

The SeqBuddy blast, bl2seq, and purge functions require access to the blastp, blastn, and blastdbcmd binaries from the NCBI C++ toolkit. If not already in your PATH, SeqBuddy.py will attempt to download the binaries if any BLAST dependant functions are called. BioPython is used heavily by the entire suite; any version earlier than 16.6 will cause unit tests to fail. PhyloBuddy requires DendroPy and version 3.0 (beta) of the ETE toolkit.

Getting started

Once installed, you can access the modules from the command line using their full names:

$: SeqBuddy -h

Or the shortcuts created by the installer:

$: sb -h

For a detailed breakdown of the tools available within each module, check out the BuddySuite wiki.

Development version installation

The easiest way to get the development version up and running is to clone/fork the repository.

$: git clone https://github.com/biologyguy/BuddySuite.git

Then move into the repo and switch to the 'development' branch:

$: cd BuddySuite
$: git checkout develop

All of the individual Buddy toolkits are located in the 'workshop' directory. The 'development' branch is where all new features are created and tested, so things may be less stable here; it's usually pretty solid though. If you're interested in contributing to the project, please ensure you are working from this branch.

See the developer page for further information on development version dependencies and how to contribute to the project.

Citation

There is a very short application note on bioRxiv that can be cited if you use BuddySuite in your work.

DOI: 10.1101/040675

Contact

Any comments you may have would be really appreciated. Please feel free to add issues in the GitHub issue tracker or contact me directly at [email protected]