Metadata-Version: 1.1
Name: dbotu
Version: 1.5.1
Summary: Distribution-based OTU calling
Home-page: http://github.com/swo/dbotu3
Author: Scott Olesen
Author-email: swo@alum.mit.edu
License: License :: OSI Approved :: MIT License
Description: Distribution-based OTU calling
        ==============================
        
        *dbotu3* is a new implementation of Sarah Preheim's dbOTU_ algorithm.  The
        scope is narrower, the numerical comparisons are faster, and the interface is
        more user-friendly.
        
        .. _dbOTU: http://aem.asm.org/content/79/21/6593.long
        
        Read the documentation_ for:
        
        - a guide to getting started,
        - an explanation of the algorithm, and
        - the API reference.
        
        .. _documentation: http://dbotu3.readthedocs.io/en/latest/
        
        You can also read our new paper_ for more technical details about the
        algorithm.  The Alm Lab website_ also has a short page with information.
        
        .. _paper: https://doi.org/10.1371/journal.pone.0176335
        .. _website: http://almlab.mit.edu/dbotu3.html
        
        Installation
        ------------
        
        dbotu3 is on PyPi_ and can be installed with pip.
        
        .. _PyPi: https://pypi.python.org/pypi/dbotu
        
        Requirements
        ------------
        
        - Numpy, SciPy, BioPython_, Pandas_
        - Levenshtein_
        
        .. _BioPython: http://biopython.org
        .. _Pandas: http://pandas.pydata.org
        .. _Levenshtein: https://pypi.python.org/pypi/python-Levenshtein
        
        Version history
        ---------------
        
        - 1.1: Corrected error where sequence IDs that could be read as integers would not be found in the table
        - 1.2: Python 2 compatibility, tox test framework, warnings for improperly-formatted sequence count tables
        - 1.2.1: Added setup requirements
        - 1.3.0: Improved OTU file header. Split the log file into a debug and progress log.
        - 1.4.0: Made an improvement to the Levenshtein-based genetic dissimilarity metric.
        - 1.4.1: Account for pandas API change to ``MultiIndex``
        - 1.5.0: Added the restart and rep seq scripts
        - 1.5.1: New function for Qiime2 compatibility
        
        To-do
        -----
        
        - Testing for the restart scripts
        - Better coverage for unit tests
        
        Citation
        --------
        
        If you use dbOTU3 in a scientific paper, we ask that you cite the
        original dbOTU publication (Preheim *et al*.) or the dbOTU3 publication:
        
        Preheim *et al*. Distribution-Based Clustering: Using Ecology To Refine the
        Operational Taxonomic Unit. *Appl Environ Microbiol* (2013) doi:10.1128/AEM.00342-13.
        
        Olesen SW, Duvallet C, and Alm EJ. dbOTU3: A new implementation of
        distribution-based OTU calling. *PLoS ONE* (2017) doi:10.1371/journal.pone.0176335.
        
        Author
        ------
        
        If you find a bug or have a request for a new feature, open an issue_.
        
        .. _issue: https://github.com/swo/dbotu3/issues
        
        Scott Olesen / *swo at alum.mit.edu*
        
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
