seq-smith
A Rust-based sequence alignment library for Python.
Installation
You can install seq-smith using pip:
pip install seq-smith
Usage
seq-smith provides several alignment functions and helper functions to make sequence alignment easy. Here's a basic example of how to perform a global alignment:
from seq_smith import global_align, make_score_matrix, encode
# Define your alphabet
alphabet = "ACGT"
# Create a scoring matrix
score_matrix = make_score_matrix(alphabet, match_score=1, mismatch_score=-1)
# Encode sequences
seqa = encode("ACGT", alphabet)
seqb = encode("AGCT", alphabet)
# Define gap penalties
gap_open = -2
gap_extend = -1
# Perform the alignment
alignment = global_align(seqa, seqb, score_matrix, gap_open, gap_extend)
# Print the alignment score
print(f"Alignment score: {alignment.score}")
# Print the alignment fragments
for frag in alignment.fragments:
print(frag)
Alignment Types
seq-smith supports the following alignment strategies:
- Global Alignment (
global_align): Uses the Needleman-Wunsch algorithm to align every residue in both sequences. - Local Alignment (
local_align): Uses the Smith-Waterman algorithm to find the best-scoring local region of similarity. - Local-Global Alignment (
local_global_align): Finds the best local alignment of the first sequence within the second, requiring the second sequence to be aligned globally. - Overlap Alignment (
overlap_align): Does not penalize gaps at the start or end of either sequence, making it ideal for finding overlaps between sequences (e.g., in sequence assembly).
Multi-threaded Alignment
seq-smith alignment functions release the GIL while computing alignments. In order to reduce overhead associated with releasing and acquiring the GIL for each alignment, seq-smith also provides *_many versions of alignment functions for 1-vs-many scenarios. This is useful when you have a query sequence and want to align it against a large number of target sequences.
Example:
from seq_smith import global_align_many
# ... setup alphabet, score_matrix, gap penalties ...
seqa = encode("ACGT", alphabet)
seqbs = [encode("ACGT", alphabet), encode("AGCT", alphabet), encode("AAAA", alphabet)]
# Align seqa against all sequences in seqbs in parallel
alignments = global_align_many(seqa, seqbs, score_matrix, gap_open, gap_extend, num_threads=4)
for aln in alignments:
print(aln.score)
1 maintainer
Metadata
1 maintainer
Release files for seq-smith 0.6.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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Built distributions (wheels)
Total release size: 8.4 MB
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