Metadata-Version: 1.1
Name: seqrecord-expanded
Version: 0.2.3
Summary: Another SeqRecord class with methods: degenerate seqs, codon positions based on reading frames, etc.
Home-page: https://github.com/carlosp420/seqrecord-expanded
Author: Carlos Peña
Author-email: mycalesis@gmail.com
License: BSD
Description: seqrecord-expanded
        ==================
        
        .. list-table::
            :stub-columns: 1
        
            * - tests
              - | |travis| |requires| |coveralls|
                | |quantified-code|
            * - package
              - |version| |wheel| |supported-versions| |supported-implementations|
        
        .. |travis| image:: https://travis-ci.org/carlosp420/seqrecord-expanded.svg?branch=master
            :alt: Travis-CI Build Status
            :target: https://travis-ci.org/carlosp420/seqrecord-expanded
        
        .. |requires| image:: https://requires.io/github/carlosp420/seqrecord-expanded/requirements.svg?branch=master
            :alt: Requirements Status
            :target: https://requires.io/github/carlosp420/seqrecord-expanded/requirements/?branch=master
        
        .. |coveralls| image:: https://coveralls.io/repos/carlosp420/seqrecord-expanded/badge.svg?branch=master&service=github
            :alt: Coverage Status
            :target: https://coveralls.io/r/carlosp420/seqrecord-expanded
        
        .. |version| image:: https://img.shields.io/pypi/v/seqrecord-expanded.svg?style=flat
            :alt: PyPI Package latest release
            :target: https://pypi.python.org/pypi/seqrecord-expanded
        
        .. |wheel| image:: https://img.shields.io/pypi/wheel/seqrecord-expanded.svg?style=flat
            :alt: PyPI Wheel
            :target: https://pypi.python.org/pypi/seqrecord-expanded
        
        .. |supported-versions| image:: https://img.shields.io/pypi/pyversions/seqrecord-expanded.svg?style=flat
            :alt: Supported versions
            :target: https://pypi.python.org/pypi/seqrecord-expanded
        
        .. |supported-implementations| image:: https://img.shields.io/pypi/implementation/seqrecord-expanded.svg?style=flat
            :alt: Supported implementations
            :target: https://pypi.python.org/pypi/seqrecord-expanded
        
        .. |quantified-code| image:: https://www.quantifiedcode.com/api/v1/project/b0bf8d6e31704c11abeb0b9043c11891/badge.svg
           :alt: Code issues
           :target: https://www.quantifiedcode.com/app/project/b0bf8d6e31704c11abeb0b9043c11891
        
        
        Another SeqRecord class with methods: degenerate seqs, codon positions based on
        reading frames, etc.
        
        Usage
        -----
        By default it assumes a DNA sequence with ambiguous characters.
        
        .. code:: python
        
            >>> from seqrecord_expanded import SeqRecordExpanded
            >>> seq_record = SeqRecordExpanded('TCTGAATGGAAGACAAAGCGTCCA',
            ...                                voucher_code='CP100-09',
            ...                                taxonomy={'genus': 'Melitaea',
            ...                                          'species': 'phoebe',
            ...                                         },
            ...                                gene_code='EF1a',
            ...                                reading_frame=1,
            ...                                table=1,  # translation table
            ...                                )
            >>> # Degenerate sequence standard genetic code
            >>> seq_record.degenerate()
            'TCNGARTGGAARACNAARMGNCCN'
            >>>
            >>> # Degenerate sequence S method
            >>> seq_record.degenerate(method='S')
            'AGYGARTGGAARACNAARMGNCCN'
            >>>
            >>> # Degenerate sequence Z method
            >>> seq_record.degenerate(method='Z')
            'TCNGARTGGAARACNAARMGNCCN'
            >>>
            >>> # Degenerate sequence SZ method
            >>> seq_record.degenerate(method='SZ')
            'NNNGARTGGAARACNAARMGNCCN'
            >>>
            >>> # get first codon positions
            >>> seq_record.first_codon_position()
            'TGTAAACC'
            >>>
            >>> # get second codon positions
            >>> seq_record.second_codon_position()
            'CAGACAGC'
            >>>
            >>> # get third codon positions
            >>> seq_record.third_codon_position()
            'TAGGAGTA'
            >>>
            >>> # get first and second positions
            >>> seq_record.first_and_second_positions()
            'TCGATGAAACAACGCC'
            >>>
            >>> # translate to aminoacid sequence
            >>> seq_record.translate()
            'SEWKTKRP'
            >>> # translate to aminoacid sequence
            >>> seq_record.translate(table=1)
            'SEWKTKRP'
        
        Installation
        ------------
        
        .. code-block:: shell
        
            pip install seqrecord-expanded
        
        Requirements
        ^^^^^^^^^^^^
        
        .. code-block:: shell
        
            pip install -r requirements.txt
        
        
        Compatibility
        -------------
        Supported Python versions: 2.6, 2.7, 3.3, 3.4, 3.5, pypy.
        
        Licence
        -------
        BSD.
        
        Authors
        -------
        
        `seqrecord-expanded` was written by `Carlos Peña <mycalesis@gmail.com>`_.
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
