Metadata-Version: 1.1
Name: bio-pm
Version: 0.1.0
Summary: A point mutation analyzing tool for nucleotide sequence
Home-page: https://github.com/ekeyme/bio-pm
Author: Ekeyme Mo
Author-email: ekeyme@gmail.com
License: MIT
Description: bio-pm
        ======
        
        .. image:: https://img.shields.io/pypi/v/bio-pm.svg
            :target: https://pypi.python.org/pypi/bio-pm
            :alt: Latest PyPI version
        
        .. image:: https://travis-ci.org/ekeyme/bio-pm.png
           :target: https://travis-ci.org/ekeyme/bio-pm
           :alt: Latest Travis CI build status
        
        A point mutation analyzing tool for nucleotide sequence
        
        Installation
        ------------
        
        Install through pip::
        
            pip install bio-pm
        
        Or manually (assuming all required modules are installed on your system)::
        
            python ./setup.py install
        
        
        Requirements
        ^^^^^^^^^^^^
        
        * Python >= 3
        * biopython
        
        Examples
        --------
        
        Analyze point mutation status using ``pm.analyze(seq, stdseq, translate=True)``
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        .. code-block:: python
        
            >>> import pm
            >>> 
            >>> seq_with_gap = 'ATGGGCG-C'
            >>> pm.analyze(seq_with_gap, stdseq)
            <pm.status.NA object with: gaps=1, nt_pm=1, aa_pm=0, stdseq='ATGGGCGC'>
            >>> 
        
        Quickly compare between ``pm.status`` objects
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ``p.status`` objects with same stdseqs have their internal order. That is ``Y > Conserved >
        PM > NA``.
        
        .. code-block:: python
        
            >>> import pm
            >>>
            >>> stdseq = "ATGGGCGCT"
            >>> seq_without_pm = 'ATGGGCGCT'
            >>> seq_conserved = "ATGGGCGCC"
            >>> seq_with_pm = 'ATGGGCGAT'
            >>> status_Y = pm.analyze(seq_without_pm, stdseq)
            >>> status_Conserved = pm.analyze(seq_conserved, stdseq)
            >>> status_PM = pm.analyze(seq_with_pm, stdseq)
            >>>
            >>> status_Y > status_Conserved > status_PM
            True
            >>>
        
        Help generate HGVS-like mutation format
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        *Codes continues from* ``Quickly compare the point mutation status objects``
        
        .. code-block:: python
        
            >>> from pm.pattern import mutant_to_str
            >>>
            >>> status_PM.pattern
            <pm.pattern.TranslatedPattern object at 0x2b03c9cfdc18>
            >>>
            >>> for nt_pm, aa_pm in status_PM.pattern.list():
            ...     print(mutant_to_str(*nt_pm) + '|' + mutant_to_str(*aa_pm))
            ...
            8C>A|3A>D
        
        Licence
        -------
        
        MIT licensed. See the bundled `LICENSE <https://github.com/ekeyme/bio-pm/blob/master/LICENSE>`_ file for more details.
        
        Authors
        -------
        
        `bio-pm` was written by `Ekeyme Mo <ekeyme@gmail.com>`_.
        
Keywords: nucleotide mutation analyzing
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3 :: Only
