C-based sequence alignment for Python
Project description
uta-align provides C-based (Cython) Needleman-Wunsch and Smith-Waterman alignment algorithms
Original author: Kevin Jacobs
IMPORTANT: Python 3.7 only for the moment (PRs welcome!)
Installation
From source:
$ python setup.py install
For Development
Install developer environment:
$ make devready
Alternatively:
$ python3 -m venv myvenv $ source myvenv/bin/activate $ make setup
Activate the environment:
$ source venv/3.7/bin/activate
(or other python version as appropriate for your system)
During development, you’ll need to recompile any code changes to the .pyx files, like this:
$ pip install -e .
Test it (in current Python environment):
$ make test ======================================== test session starts ======================================== platform linux -- Python 3.7.5, pytest-5.3.5, py-1.8.1, pluggy-0.13.1 rootdir: /home/reece/projects/biocommons/uta-align, inifile: setup.cfg, testpaths: tests collected 5 items tests/test_align_algorithms.py . [ 20%] tests/test_align_gap_open.py .. [ 60%] tests/test_cigar_utils.py . [ 80%] tests/test_nw.py . [100%] ========================================= 5 passed in 0.12s =========================================
Tox test it (in multiple environments:
$ make tox GLOB sdist-make: /home/reece/projects/biocommons/uta-align/setup.py py37 inst-nodeps: /home/reece/projects/biocommons/uta-align/.tox/.tmp/package/... ... py37: commands succeeded congratulations :)
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