Metadata-Version: 1.1
Name: py-gfe
Version: 1.1.4
Summary: Python package for converting sequence annotations to gene feature enumerations (GFE).
Home-page: https://github.com/nmdp-bioinformatics/py-gfe
Author: CIBMTR
Author-email: cibmtr-pypi@nmdp.org
License: LGPL 3.0
Description: ===============================
        py-gfe
        ===============================
        
        
        .. image:: https://img.shields.io/pypi/v/pygfe.svg
                :target: https://pypi.python.org/pypi/pygfe
        
        .. image:: https://img.shields.io/travis/mhalagan-nmdp/pygfe.svg
                :target: https://travis-ci.org/mhalagan-nmdp/pygfe
        
        .. image:: https://readthedocs.org/projects/pygfe/badge/?version=latest
                :target: https://pygfe.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        .. image:: https://pyup.io/repos/github/mhalagan-nmdp/pygfe/shield.svg
             :target: https://pyup.io/repos/github/mhalagan-nmdp/pygfe/
             :alt: Updates
        
        
        Python Boilerplate contains all the boilerplate you need to create a Python package.
        
        
        * Free software: LGPL 3.0
        * Documentation: https://pygfe.readthedocs.io.
        
        Docker
        --------
        
        .. code-block:: shell
        
          docker pull nmdpbioinformatics/py-gfe
        
        .. code-block:: 
        
        	docker run -it --rm -v $PWD:/opt nmdpbioinformatics/py-gfe seq2gfe \
        		-f /opt/your_fastafile.fasta -l HLA-A
        
        
        Example
        --------
        
        .. code-block:: python3
        
            >>> from Bio import SeqIO
            >>> from BioSQL import BioSeqDatabase
            >>> from seqann.sequence_annotation import BioSeqAnn
            >>> import pygfe
            >>> seq_file = 'test_dq.fasta'
            >>> gfe = pygfe.pyGFE()
            >>> server = BioSeqDatabase.open_database(driver="pymysql", user="root",
            ...                                       passwd="", host="localhost",
            ...                                      db="bioseqdb")
            >>> seqann = BioSeqAnn(server=server)
            >>> seq_rec = list(SeqIO.parse(seq_file, 'fasta'))[0]
            >>> annotation = seqann.annotate(seq_rec, "HLA-DQB1")
            >>> gfe = gfe.get_gfe(annotation, "HLA-DQB1")
            >>> print(gfe)
            HLA-DQB1w0-4-0-141-0-12-0-4-0-0-0-0-0
        
        Credits
        ---------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        
        =======
        History
        =======
        
        0.0.1 (2017-11-09)
        ------------------
        
        * First release on PyPI.
        
        
Keywords: pygfe
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
