biocommons / uta-align

C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.

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 :)