uta-align 0.2.0a3

C-based sequence alignment for Python

uta-align provides C-based (Cython) Needleman-Wunsch and Smith-Waterman alignment algorithms

Original author: Kevin Jacobs

Important

Python 3.6+ only

Installation

From source:

$ python setup.py install

For Development

• Install developer environment:

  $ make devready

• 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/1/uta-align-1.1.13a2.dev7+g98b7cc9.d20200303.zip
  ...
  py37: commands succeeded
  congratulations :)