py-gfe
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/py-gfedocker run -it --rm -v $PWD:/opt nmdpbioinformatics/py-gfe seq2gfe \
-f /opt/your_fastafile.fasta -l HLA-AExample
>>> 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-DQB1w0-4-0-141-0-12-0-4-0-0-0-0-0Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.0.1 (2017-11-09)
First release on PyPI.
1 maintainer
Metadata
1 maintainer
Release files for py-gfe 1.1.6
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| py-gfe-1.1.6.tar.gz | 70.6 kB | Without provenance | Details for py-gfe-1.1.6.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| py_gfe-1.1.6-py2.py3-none-any.whl | Python 3, Python 2 | none | any | Details for py_gfe-1.1.6-py2.py3-none-any.whl |
Total release size: 135.5 kB
Release files / py-gfe-1.1.6.tar.gz
| Download URL | py-gfe-1.1.6.tar.gz |
|---|---|
| Size | 70.6 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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Release files / py_gfe-1.1.6-py2.py3-none-any.whl
| Download URL | py_gfe-1.1.6-py2.py3-none-any.whl |
|---|---|
| Size | 64.9 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
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twine/4.0.2 CPython/3.12.0
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