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