Metadata-Version: 2.1
Name: py-gfe
Version: 1.1.2
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
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
Requires-Dist: seq-ann (==1.1.0)
Requires-Dist: more-itertools (==8.7.0)
Requires-Dist: neo4j-driver (==1.7.4)
Requires-Dist: py2neo (==4.3.0)
Requires-Dist: pandas (>=1.2.3)

===============================
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.



