Metadata-Version: 2.0
Name: pygfe
Version: 0.0.26
Summary: Python package for converting sequence annotations to gene feature enumerations (GFE).
Home-page: https://github.com/mhalagan-nmdp/pygfe
Author: Mike Halagan
Author-email: mhalagan@nmdp.org
License: LGPL 3.0
Description-Content-Type: UNKNOWN
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 :: 2
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
Requires-Dist: atomicwrites (==1.1.5)
Requires-Dist: attrs (==18.1.0)
Requires-Dist: biopython (==1.70)
Requires-Dist: bson (==0.5.5)
Requires-Dist: certifi (==2017.11.5)
Requires-Dist: chardet (==3.0.4)
Requires-Dist: click (==6.7)
Requires-Dist: colorama (==0.3.9)
Requires-Dist: idna (==2.6)
Requires-Dist: more-itertools (==4.2.0)
Requires-Dist: neo4j-driver (==1.6.1)
Requires-Dist: neotime (==1.0.0)
Requires-Dist: numpy (==1.13.3)
Requires-Dist: pandas (==0.22.0)
Requires-Dist: pkginfo (==1.4.1)
Requires-Dist: pluggy (==0.6.0)
Requires-Dist: prompt-toolkit (==1.0.15)
Requires-Dist: py (==1.5.4)
Requires-Dist: py2neo (==4.0.0)
Requires-Dist: Pygments (==2.2.0)
Requires-Dist: PyMySQL (==0.7.11)
Requires-Dist: pytest (==3.6.3)
Requires-Dist: python-dateutil (==2.6.1)
Requires-Dist: pytz (==2017.3)
Requires-Dist: requests (==2.18.4)
Requires-Dist: requests-toolbelt (==0.8.0)
Requires-Dist: seqann
Requires-Dist: six (==1.11.0)
Requires-Dist: tqdm (==4.19.4)
Requires-Dist: twine (==1.9.1)
Requires-Dist: urllib3 (==1.22)
Requires-Dist: wcwidth (==0.1.7)

===============================
pyGFE
===============================


.. 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
--------
* docker pull nmdpbioinformatics/pygfe

.. code-block:: 

	docker run -it --rm -v $PWD:/opt nmdpbioinformatics/pygfe 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.



