swalign

This package implements a Smith-Waterman style local alignment algorithm. You can align a query sequence to a reference. The scoring functions can be based on a matrix, or simple identity. Weights can be adjusted for match/mismatch and gaps, with gap extention penalties. Additionally, the gap penalty can be subject to a decay to prioritize long gaps.

The input files are FASTA format sequences, or strings of sequences.

Here is some skeleton code to get you started:

    import swalign
    # choose your own values here… 2 and -1 are common.
    match = 2
    mismatch = -1
    scoring = swalign.NucleotideScoringMatrix(match, mismatch)

    sw = swalign.LocalAlignment(scoring)  # you can also choose gap penalties, etc...
    alignment = sw.align('ACACACTA','AGCACACA')
    alignment.dump()

To cythonize this package for accelerated use, run the following and copy the .so file to the desired python library path.

python setup.py build_ext --inplace

For other uses, see the script in bin/swalign or https://compgen.io/projects/swalign