{ "info": { "author": "Scott Sherrill-Mix", "author_email": "shescott@upenn.edu", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License (GPL)", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "ampCountPy\n==========\n.. image:: https://travis-ci.org/sherrillmix/ampCountPy.svg?branch=master\n :alt: Travis CI\n :target: https://travis-ci.org/sherrillmix/ampCountPy\n.. image:: https://codecov.io/github/sherrillmix/ampCountPy/coverage.svg?branch=master\n :alt: Codecov\n :target: https://codecov.io/github/sherrillmix/ampCountPy?branch=master\n.. image:: https://badge.fury.io/py/ampcountpy.svg\n :alt: PyPi version\n :target: https://badge.fury.io/py/ampcountpy\n\n\nSome python functions to count the expected amplifications for genomic regions given a set of primer binding locations for a `multiple displacement amplification `_ reaction. See `ampCountR `_ for more details.\n \nInstallation\n------------\nEasy install\n~~~~~~~~~~~~\n\nThe easy way to install is to just do::\n\n pip install ampcountpy\n\nGithub\n~~~~~~\n\nTo install the development version from github, clone the repository to a local directory using something like::\n\n git clone https://github.com/sherrillmix/ampcountpy.git\n\nand run `setup.py` from the resulting directory (the `--user` installs it locally and doesn't require root access)::\n\n cd ampcountpy\n python setup.py install --user\n python setup.py test\n\nRun directly\n------------\nThe module can be called directly using something like::\n\n python -m ampcountpy -f forward.txt -r reverse.txt\n\nor::\n\n ampcountpy -f forward.txt -r reverse.txt\n\nwhere `forward.txt` is a text file containing position of primer landing sites on the forward strand and `reverse.txt` is primer landing sites on the reverse strand. By default, amplification predictions are output to out.csv. The full details on options and arguments is available with::\n\n ampcountpy --help\n\nUsing function in python\n------------------------\nThe main function is `predictAmplifications` which can be used like:\n\n.. code:: python\n\n from ampcountpy import predictAmplifications\n forwards=[1,2,3]\n reverses=[5,6,7]\n predictions=predictAmplifications(forwards,reverses)\n\nwhere `forwards` are the 5'-most base of primer landing sites on the forward strand and `reverses` are the 3'-most base of primers landing on the reverse strand.\n\n\nChangelog\n---------\n0.2.0 (2015-12-08)\n\n* Count non-overlapping primers correctly\n\n0.1.3 (2015-11-02)\n\n* Fix header\n\n0.1.2 (2015-11-02)\n\n* Fix changelog formatting\n\n0.1.1 (2015-11-02)\n\n* Pip install instructions\n\n0.1.0 (2015-11-02)\n\n* Initial public release", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": 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