sassy-rs 0.2.0

Fast approximate string searching using SIMD

Sassy Python Bindings

🐍 The python bindings for Sassy

Installation

Pip.

pip install sassy-rs

(as sassy was already taken we chose sassy-rs)

From source. In the root of the repository, run:

maturin develop --features python

You need Maturin for this, see maturin:

Usage

A simple usage is as follows:

import sassy
pattern = b"ATCGATCG"
text = b"GGGGATCGATCGTTTT"
# alphabet: ascii, dna, uipac
searcher = sassy.Searcher("dna")
matches = searcher.search(pattern, text, k=1)
for i, match in enumerate(matches):
    print(f"Match {i+1}:")
    print(f"    Start: {match.text_start}")
    print(f"    End: {match.text_end}")
    print(f"    Cost: {match.cost}")
    print(f"    Strand: {match.strand}")
    print(f"    CIGAR: {match.cigar}")

This finds 3 matches:

Match 1:
    Start: 4
    End: 12
    Cost: 0
    Strand: +
    CIGAR: 8=
Match 2:
    Start: 6
    End: 14
    Cost: 1
    Strand: -
    CIGAR: 6=X=
Match 3:
    Start: 2
    End: 10
    Cost: 1
    Strand: -
    CIGAR: X7=

Further options are sassy.Searcher(alpha=0.5) to allow overhang alignments, and sassy.Searcher("dna", rc=False) to disable reverse complements for DNA or IUPAC strings. searcher.search is the simple function to search one pattern in one text, while searcher.search_many takes multiple patterns and multiple texts and searches each pattern in each text, possibly in multiple threads.

See sassy/example.py for a larger example.

Troubleshooting

1. I could install sassy-rc but no modules/functions are found.

When creating an issue please include the output of print(dir(sassy)) if you were able to install sassy-rs but no functions/modules were found.

Your output might look like:

['__all__', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__']

Whereas it should look like:

['Searcher', '__all__', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', 'features', 'sassy']

2. Other sassy issues.

If you were able to install sassy, but have other issues please also add the output of sassy.features().