Metadata-Version: 1.1
Name: ampcountpy
Version: 0.1.3
Summary: Some functions to count the expected amplifications for genomic regions given a set of primer binding locations for a multiple displacement amplification reaction.
Home-page: http://github.com/sherrillmix/ampCountPy
Author: Scott Sherrill-Mix
Author-email: shescott@upenn.edu
License: GPL 3
Description: ampCountPy
        ==========
        .. image:: https://travis-ci.org/sherrillmix/ampCountPy.svg?branch=master
            :alt: Travis CI
            :target: https://travis-ci.org/sherrillmix/ampCountPy
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            :alt: Codecov
            :target: https://codecov.io/github/sherrillmix/ampCountPy?branch=master
        .. image:: https://badge.fury.io/py/ampcountpy.svg
            :alt: PyPi version
            :target: https://badge.fury.io/py/ampcountpy
        
        
        Some python functions to count the expected amplifications for genomic regions given a set of primer binding locations for a `multiple displacement amplification <http://en.wikipedia.org/wiki/Multiple_displacement_amplification>`_ reaction. See `ampCountR <https://github.com/sherrillmix/ampCountR>`_ for more details.
         
        Installation
        ------------
        Easy install
        ~~~~~~~~~~~~
        
        The easy way to install is to just do::
        
          pip install ampcountpy
        
        Github
        ~~~~~~
        
        To install the development version from github, clone the repository to a local directory using something like::
        
            git clone https://github.com/sherrillmix/ampcountpy.git
        
        and run `setup.py` from the resulting directory (the `--user` installs it locally and doesn't require root access)::
        
          cd ampcountpy
          python setup.py test
          python setup.py install --user
        
        Run directly
        ------------
        The module can be called directly using something like::
        
          python -m ampcountpy -f forward.txt -r reverse.txt
        
        or::
        
          ampcountpy -f forward.txt -r reverse.txt
        
        where `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::
        
          ampcountpy --help
        
        Using function in python
        ------------------------
        The main function is `predictAmplifications` which can be used like:
        
        ..  code:: python
        
          from ampcountpy import predictAmplifications
            forwards=[1,2,3]
            reverses=[5,6,7]
            predictions=predictAmplifications(forwards,reverses)
        
        where `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.
        
        
        Changelog
        ---------
        0.1.3 (2015-11-02)
        
        * Fix header
        
        0.1.2 (2015-11-02)
        
        * Fix changelog formatting
        
        0.1.1 (2015-11-02)
        
        * Pip install instructions
        
        0.1.0 (2015-11-02)
        
        * Initial public release
        
        
        
        
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
