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