Metadata-Version: 1.1
Name: dataset-creator
Version: 0.3.1
Summary: Takes SeqRecordExpanded objects and creates datasets for phylogenetic software
Home-page: https://github.com/carlosp420/dataset-creator
Author: Carlos Peña
Author-email: mycalesis@gmail.com
License: BSD
Description: .. image:: https://rawgit.com/carlosp420/dataset-creator/master/media/logo.svg
            :width: 240px
            :align: center
            :alt: Dataset-creator
        
        =========================================
        Dataset creator for phylogenetic software
        =========================================
        
        .. 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/dataset-creator.svg?branch=master
            :alt: Travis-CI Build Status
            :target: https://travis-ci.org/carlosp420/dataset-creator
        
        .. |requires| image:: https://requires.io/github/carlosp420/dataset-creator/requirements.svg?branch=master
            :alt: Requirements Status
            :target: https://requires.io/github/carlosp420/dataset-creator/requirements/?branch=master
        
        .. |coveralls| image:: https://coveralls.io/repos/carlosp420/dataset-creator/badge.svg?branch=master&service=github
            :alt: Coverage Status
            :target: https://coveralls.io/r/carlosp420/dataset-creator
        
        .. |version| image:: https://img.shields.io/pypi/v/dataset-creator.svg?style=flat
            :alt: PyPI Package latest release
            :target: https://pypi.python.org/pypi/dataset-creator
        
        .. |wheel| image:: https://img.shields.io/pypi/wheel/dataset-creator.svg?style=flat
            :alt: PyPI Wheel
            :target: https://pypi.python.org/pypi/dataset-creator
        
        .. |supported-versions| image:: https://img.shields.io/pypi/pyversions/dataset-creator.svg?style=flat
            :alt: Supported versions
            :target: https://pypi.python.org/pypi/dataset-creator
        
        .. |supported-implementations| image:: https://img.shields.io/pypi/implementation/dataset-creator.svg?style=flat
            :alt: Supported implementations
            :target: https://pypi.python.org/pypi/dataset-creator
        
        .. |quantified-code| image:: https://www.quantifiedcode.com/api/v1/project/f059ab475f2547758722b80ea528c457/badge.svg
          :target: https://www.quantifiedcode.com/app/project/f059ab475f2547758722b80ea528c457
          :alt: Code issues
        
        Takes SeqRecordExpanded objects and creates datasets for phylogenetic software
        
        * Free software: BSD license
        
        Installation
        ============
        
        ::
        
            pip install dataset_creator
        
        Usage
        =====
        The list of SeqRecordExpanded objects should be sorted by gene_code first then
        by voucher_code.
        
        .. code-block:: python
        
            >>> from seqrecord_expanded import SeqRecord
            >>> from dataset_creator import Dataset
            >>>
            >>> # `table` is the Translation Table code based on NCBI
            >>> seq_record1 = SeqRecord('ACTACCTA', reading_frame=2, gene_code='RpS5',
            ...                         table=1, voucher_code='CP100-10',
            ...                         taxonomy={'genus': 'Aus', 'species': 'bus'})
            >>>
            >>> seq_record2 = SeqRecord('ACTACCTA', reading_frame=2, gene_code='RpS5',
            ...                         table=1, voucher_code='CP100-10',
            ...                         taxonomy={'genus': 'Aus', 'species': 'bus'})
            >>>
            >>> seq_record3 = SeqRecord('ACTACCTA', reading_frame=2, gene_code='wingless',
            ...                         table=1, voucher_code='CP100-10',
            ...                         taxonomy={'genus': 'Aus', 'species': 'bus'})
            >>>
            >>> seq_record4 = SeqRecord('ACTACCTA', reading_frame=2, gene_code='winglesss',
            ...                         table=1, voucher_code='CP100-10',
            ...                         taxonomy={'genus': 'Aus', 'species': 'bus'})
            >>>
            >>> seq_records = [
            ...    seq_record1, seq_record2, seq_record3, seq_record4,
            ... ]
            >>> # codon positions can be 1st, 2nd, 3rd, 1st-2nd, ALL (default)
            >>> dataset = Dataset(seq_records, format='NEXUS', partitioning='by gene',
            ...                   codon_positions='1st',
            ...                   )
            >>> print(dataset.dataset_str)
            """#NEXUS
            blah blah
            """
        
        
        
        Development
        ===========
        
        To run the all tests run::
        
            tox
        
        Changelog
        =========
        
        0.3.1 (2015-10-01)
        ------------------
        * Fixed bug that raised an exception when user wanted partitioned dataset by
          codon positions of only one codon.
        
        0.3.0 (2015-10-01)
        ------------------
        * Accepts voucher code as string that will be used to generate the outgroup
          string needed for NEXUS and TNT files.
        
        0.2.0 (2015-09-30)
        ------------------
        * Creates datasets as degenerated sequences using the method by Zwick et al.
        
        0.1.1 (2015-09-30)
        ------------------
        
        * It will issue errors if reading frames are not specified unless they
          are strictly necessary to build the dataset (datasets need to be divided by
          codon positions).
        * Added documentation using sphinx-doc
        * Creates datasets as aminoacid sequences.
        
        0.1.0 (2015-09-23)
        ------------------
        
        * Creates Nexus, Tnt, Fasta, Phylip and Mega dataset formats.
        
        0.0.1 (2015-06-10)
        ------------------
        
        * First release on PyPI.
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
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 :: Utilities
