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 :)
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
uta-align-0.3.0.tar.gz
(340.1 kB
view details)
File details
Details for the file uta-align-0.3.0.tar.gz.
File metadata
- Download URL: uta-align-0.3.0.tar.gz
- Upload date:
- Size: 340.1 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.0.0 CPython/3.11.6
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 3b51b0b85ea8da5d7b5a23bdb9c29566304ec7c5ab3e3954a2f461c7f6abfa6c |
|
| MD5 | 35623c09b769a1fdba0f54af86c8940f |
|
| BLAKE2b-256 | d6b500fdbe4f2fb1b734bc5bbc0ae26ae7562b5c202fdd72457d8cf3bdd36b79 |
