Versalign is Python package that allows you to create multiple sequence alignments for arbitrary lists of objects.

💪 Getting Started

Pairwise alignment:

from versalign.motif import Motif
from versalign.pairwise import PairwiseAlignment, align_pairwise
from versalign.sequence import Sequence

class A(Motif):
    def __eq__(self, other):
        return isinstance(other, A)
    
    def __str__(self):
        return "A"

class B(Motif):
    def __eq__(self, other):
        return isinstance(other, B)
    
    def __str__(self):
        return "B"

def score_func(a, b):
    if a == b:
        return 1
    return -1

seq_a = Sequence("seq_a", [A(), A(), A()])
seq_b = Sequence("seq_b", [B(), B(), B()])

aligned_seq_a, aligned_seq_b, score = align_pairwise(
    seq_a=seq_a,
    seq_b=seq_b,
    score_func=score_func,
    algorithm=PairwiseAlignment.NEEDLEMAN_WUNSCH,
    options={"gap_penalty": 2, "end_gap_penalty": 1},
)

print(aligned_seq_a)
print(aligned_seq_b)

>> AAA---
>> ---BBB

Multiple sequence alignment:

from versalign.msa import multiple_sequence_alignment

seq_a = Sequence("seq_a", [A(), A(), A()])
seq_b = Sequence("seq_b", [B(), B(), B()])
seq_c = Sequence("seq_c", [A(), B(), B()])

result = multiple_sequence_alignment(
    seqs=[seq_a, seq_b, seq_c],
    gap_penalty=2,
    end_gap_penalty=1,
    score_func=score_func,
)

for seq in result:
    print(seq)

>> ---BBB
>> --ABB-
>> AAA---

🚀 Installation

The most recent release can be installed from PyPI with:

pip install versalign

The most recent code and data can be installed directly from GitHub with:

pip install git+https://github.com/davidmeijer/versalign.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

git clone git+https://github.com/davidmeijer/versalign.git
cd versalign
pip install -e .

🥼 Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

tox -e finish

This script does the following:

1. Uses Bump2Version to switch the version number in the setup.cfg, src/versalign/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using build
3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion -- minor after.