pyGFE

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

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.

Metadata

Release files for pygfe 0.0.32

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Built distribution (wheel)

Table of built distributions (wheels) for pygfe 0.0.32
File	Interpreter	ABI	Platform	Actions Reset
pygfe-0.0.32-py2.py3-none-any.whl 42.6 kB Sep 25, 2018 Without provenance	Python 3, Python 2	none	any	Details for pygfe-0.0.32-py2.py3-none-any.whl

Release files / pygfe-0.0.32-py2.py3-none-any.whl

Download URL	pygfe-0.0.32-py2.py3-none-any.whl
Size	42.6 kB
Tags	Python 2 Python 3
SHA-256 checksum How to use checksums	`70d1dfc9b4d58f7c1cb8ce9142f9772a376ed8d32751db24cd87f3fdf6af5a00`
BLAKE2b-256 checksum How to use checksums	`b43e8442612256b6aac975ff9c3216dabf9a51e68316cce7bbcd3eba333d78d5`
Upload date	Sep 25, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/1.9.1 pkginfo/1.4.1 requests/2.18.4 setuptools/36.7.1 requests-toolbelt/0.8.0 tqdm/4.19.4 CPython/3.6.0`

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