Create GFE from consensus sequences
1.2K
.. image:: https://img.shields.io/pypi/v/pygfe.svg :target: https://pypi.python.org/pypi/pygfe
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Python Boilerplate contains all the boilerplate you need to create a Python package.
.. code-block::
docker run -it --rm -v $PWD:/opt nmdpbioinformatics/pygfe seq2gfe \
-f /opt/your_fastafile.fasta -l HLA-A
.. 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
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
Content type
Image
Digest
Size
332.5 MB
Last updated
almost 9 years ago
docker pull nmdpbioinformatics/pygfe