{ "info": { "author": "Scott Olesen", "author_email": "swo@alum.mit.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Distribution-based OTU calling\n==============================\n\n*dbotu3* is a new implementation of Sarah Preheim's dbOTU_ algorithm. The\nscope is narrower, the numerical comparisons are faster, and the interface is\nmore user-friendly.\n\n.. _dbOTU: http://aem.asm.org/content/79/21/6593.long\n\nRead the documentation_ for:\n\n- a guide to getting started,\n- an explanation of the algorithm, and\n- the API reference.\n\n.. _documentation: http://dbotu3.readthedocs.io/en/latest/\n\nYou can also read our new paper_ for more technical details about the\nalgorithm. The Alm Lab website_ also has a short page with information.\n\n.. _paper: https://doi.org/10.1371/journal.pone.0176335\n.. _website: http://almlab.mit.edu/dbotu3.html\n\nInstallation\n------------\n\ndbotu3 is also on conda_ and can be installed as follows:\n\n.. _conda: https://anaconda.org/cduvallet/dbotu\n\n.. code-block::\n\n conda install -c cduvallet -c conda-forge dbotu\n\nFor `QIIME 2`_ users, dbotu3 is also available as a plugin_.\n\n.. _plugin: https://github.com/cduvallet/q2-dbotu\n.. _`QIIME 2`: https://qiime2.org/\n\nThe PyPi_ package is no longer update.\n\n.. _PyPi: https://pypi.python.org/pypi/dbotu\n\nRequirements\n------------\n\n- Numpy, SciPy, BioPython_, Pandas_\n- Levenshtein_\n\n.. _BioPython: http://biopython.org\n.. _Pandas: http://pandas.pydata.org\n.. _Levenshtein: https://pypi.python.org/pypi/python-Levenshtein\n\nVersion history\n---------------\n\n- 1.1: Corrected error where sequence IDs that could be read as integers would not be found in the table\n- 1.2: Python 2 compatibility, tox test framework, warnings for improperly-formatted sequence count tables\n- 1.2.1: Added setup requirements\n- 1.3.0: Improved OTU file header. Split the log file into a debug and progress log.\n- 1.4.0: Made an improvement to the Levenshtein-based genetic dissimilarity metric.\n- 1.4.1: Account for pandas API change to ``MultiIndex``\n- 1.5.0: Added the restart and rep seq scripts\n- 1.5.1: New function for Qiime2 compatibility\n- 1.5.2: Move files around to make this a Python package (rather than dbotu.py script)\n- 1.5.3: Point to conda, rather than PyPi, installation\n\nTo-do\n-----\n\n- Testing for the restart scripts\n- Better coverage for unit tests\n\nCitation\n--------\n\nIf you use dbOTU3 in a scientific paper, we ask that you cite the\noriginal dbOTU publication (Preheim *et al*.) or the dbOTU3 publication:\n\nPreheim *et al*. Distribution-Based Clustering: Using Ecology To Refine the\nOperational Taxonomic Unit. *Appl Environ Microbiol* (2013) doi:10.1128/AEM.00342-13.\n\nOlesen SW, Duvallet C, and Alm EJ. dbOTU3: A new implementation of\ndistribution-based OTU calling. *PLoS ONE* (2017) doi:10.1371/journal.pone.0176335.\n\nAuthor\n------\n\nIf you find a bug or have a request for a new feature, open an issue_.\n\n.. _issue: https://github.com/almlab/dbotu3/issues\n\nScott Olesen / *swo at alum.mit.edu*\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://github.com/swo/dbotu3", "keywords": "", "license": "License :: OSI Approved :: MIT License", "maintainer": "", "maintainer_email": "", "name": "dbotu", "package_url": "https://pypi.org/project/dbotu/", "platform": "any", "project_url": "https://pypi.org/project/dbotu/", "project_urls": { "Homepage": "http://github.com/swo/dbotu3" }, 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