Skip to main content

Python package for converting sequence annotations to gene feature enumerations (GFE).

Project description

pyGFE

https://img.shields.io/pypi/v/pygfe.svg https://img.shields.io/travis/mhalagan-nmdp/pygfe.svg Documentation Status Updates

Python Boilerplate contains all the boilerplate you need to create a Python package.

Docker

  • docker pull nmdpbioinformatics/pygfe

docker run -it --rm -v $PWD:/opt nmdpbioinformatics/pygfe seq2gfe \
        -f /opt/your_fastafile.fasta -l HLA-A

Example

>>> 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.

History

0.0.1 (2017-11-09)

  • First release on PyPI.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distributions

No source distribution files available for this release.See tutorial on generating distribution archives.

Built Distribution

pygfe-0.0.32-py2.py3-none-any.whl (42.6 kB view hashes)

Uploaded Python 2 Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page