Metadata-Version: 1.1
Name: seqrecord_expanded
Version: 0.0.2
Summary: BioPython's SeqRecord class, but expanded with additional 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: UNKNOWN
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        seqrecord-expanded
        ==================
        
        BioPython's SeqRecord class, but expanded with additional 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
            >>> seq_record.translate()
            OKPDOR
        
        Installation
        ------------
        
        .. code-block:: shell
        
            pip install seqrecord-expanded
        
        Requirements
        ^^^^^^^^^^^^
        Python3.
        
        .. code-block:: shell
        
            pip install -r requirements.txt
        
        
        Compatibility
        -------------
        
        Licence
        -------
        BSD.
        
        Authors
        -------
        
        `seqrecord-expanded` was written by `Carlos Peña <mycalesis@gmail.com>`_.
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.4
