Metadata-Version: 1.2
Name: buddysuite
Version: 1.4.0
Summary: BuddySuite is a collection of command line utilities written in Python for working with biological data.
Home-page: https://github.com/biologyguy/BuddySuite
Author: Stephen Bond
Author-email: biologyguy@gmail.com
Maintainer: Stephen Bond
License: Public Domain
Description: |Build_Status| |Coverage_Status| |PyPi_version|
        
        |BuddySuite|
        
        --------------
        
        Description
        -----------
        
        The BuddySuite modules are 'one-stop-shop' command-line tools for common
        biological data file manipulations. Formats are detected automatically,
        conversions are seamless, and you can pipe into or out of the modules to
        build custom bioinformatics workflows, allowing you to spend more time analyzing
        your sequences, alignments, and phylogenetic trees, instead of wrangling them.
        
        For example, the following command reads in three sequence files (all in
        different formats), pulls out records with RefSeq identifiers, calls
        MAFFT to generate an alignment, shifts gaps to force a codon alignment,
        calls RAxML to infer a phylogeny, and then roots the tree at its
        midpoint.
        
        ``$: ﻿seqbuddy seqs1.gb seqs2.embl seqs3.fasta --pull_records "[XN]M" | alignbuddy --generate_alignment mafft | alignbuddy --enforce_triplets | phylobuddy --generate_tree raxmlHPC-SSE3 | phylobuddy --root``
        
        BuddySuite is a Python3 project, developed and extensively tested on
        Linux and Mac OS X. Full release versions are also tested on Windows
        before release, so should work as expected on Vista and above.
        
        Getting started
        ---------------
        
        The simplest way to get up and running is:
        
        .. code:: bash
        
            $: pip install buddysuite
            $: buddysuite -setup
        
        Further instructions are available in the `installation
        guide <https://github.com/biologyguy/BuddySuite/wiki/Installation-Guide>`__.
        
        There is also a `Beginners'
        Guide <https://github.com/biologyguy/BuddySuite/wiki/Beginners-Guide>`__
        to show you the basics, as well as a more comprehensive
        `Tutorial <https://github.com/biologyguy/BuddySuite/wiki/Tutorial>`__.
        
        Each tool in the BuddySuite has been extensively documented in the
        `wiki <https://github.com/biologyguy/BuddySuite/wiki>`__, complete with
        worked examples and explanations for all arguments/options.
        
        -  `SeqBuddy <https://github.com/biologyguy/BuddySuite/wiki/SeqBuddy>`__
        -  `AlignBuddy <https://github.com/biologyguy/BuddySuite/wiki/AlignBuddy>`__
        -  `PhyloBuddy <https://github.com/biologyguy/BuddySuite/wiki/PhyloBuddy>`__
        -  `DatabaseBuddy <https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy>`__
        
        Developers
        ----------
        
        All of the individual Buddy toolkits are located in the 'buddysuite'
        directory and the `'develop'
        branch <https://github.com/biologyguy/BuddySuite/tree/develop>`__ is
        where all new features have been implemented. If you're interested in
        contributing, please refer to the `developer
        page <https://github.com/biologyguy/BuddySuite/wiki/Developers>`__ for
        further information.
        
        Citation
        --------
        
        If you use BuddySuite in your work, we would greatly appreciate references to our manuscript:
        
        .. code:: bibtex
        
           @article{doi:10.1093/molbev/msx089,
           author = {Bond, Stephen R. and Keat, Karl E. and Barreira, Sofia N. and Baxevanis, Andreas D.},
           title = {BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees},
           journal = {Molecular Biology and Evolution},
           volume = {34},
           number = {6},
           pages = {1543-1546},
           year = {2017},
           doi = {10.1093/molbev/msx089},
           URL = { + http://dx.doi.org/10.1093/molbev/msx089},
           eprint = {/oup/backfile/content_public/journal/mbe/34/6/10.1093_molbev_msx089/1/msx089.pdf}
           }
        
        Through a series of unfortunate events and a surprisingly unresponsive publishing company, the manuscript is behind a
        paywall... Thank goodness for `pre-prints on bioRxiv <https://doi.org/10.1101/040675>`__ !
        
        |DOI|
        
        Contact
        -------
        
        Any comments you have would be really appreciated. Please feel free to
        add issues in the GitHub issue tracker or contact Steve Bond (lead
        developer) directly at biologyguy@gmail.com.
        
        .. |Build_Status| image:: https://travis-ci.com/biologyguy/BuddySuite.svg?branch=master
           :target: https://travis-ci.com/biologyguy/BuddySuite
        .. |Coverage_Status| image:: https://img.shields.io/coveralls/biologyguy/BuddySuite/master.svg
           :target: https://coveralls.io/github/biologyguy/BuddySuite?branch=master
        .. |PyPi_version| image:: https://img.shields.io/pypi/v/buddysuite.svg
           :target: https://pypi.python.org/pypi/buddysuite
        .. |BuddySuite| image:: https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/BuddySuite-logo.png
           :target: https://github.com/biologyguy/BuddySuite/wiki
           :height: 200 px
        .. |DOI| image:: https://img.shields.io/badge/doi-10.1093/molbev/msx089-blue.svg?style=flat
           :target: https://doi.org/10.1101/040675
        
Keywords: computational biology,computational genetics,genetics,genome,phylogenetics,biology,bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: Public Domain
Classifier: Natural Language :: English
Classifier: Environment :: Console
