Modern C++ Binding for SSW Library

Changes

• Add Modern C++ Binding
• Use pybind11 Binding
• Provide Python api

Installation

$ pip install mssw

Benchmark

The result is tested in Linux x86_64 4 cores and 4GB of memory.

With BioPython

Query Length	Reference Length	mssw Time (s)	bio python Time (s)	Speedup
15	39	4.470348e-05	1.424551e-04	3.186666
150	390	2.179623e-04	2.270699e-03	10.41785
1500	3900	1.665862e-02	1.534623e-01	9.212187
15000	39000	1.696888e+00	1.574137e+01	9.276609

Usage

Example 1: Alignment with default filter and score matrix

import mssw

reference = "CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA"
query = "CTGAGCCGGTAAATC"
# default match: int = 2, mismatch: int = 2, gap_open: int = 3, gap_extend: int = 1
aligner = mssw.Aligner()
aligner_filter = mssw.Filter()
alignment = aligner.align(query, reference, aligner_filter)

Example 2: Alignment with default filter and score matrix

import mssw

reference = "CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA"
query = "CTGAGCCGGTAAATC"
aligner = mssw.Aligner()
alignment = aligner.align(query, reference)

Example 3: Alignment with filter But custom gap open and gap extension

import mssw

reference = "CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA"
query = "CTGAGCCGGTAAATC"
aligner = mssw.Aligner(match=3, mismatch=1, gap_open=2, gap_extend=2)
alignment = aligner.align(query, reference)

Example 4: Alignment Result

import mssw

reference = "CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA"
query = "CTGAGCCGGTAAATC"
aligner = mssw.Aligner(match=3, mismatch=1, gap_open=2, gap_extend=2)
alignment = aligner.align(query, reference)

assert alignment.sw_score == 21
assert alignment.sw_score_next_best == 2
assert alignment.ref_begin == 8
assert alignment.ref_end == 21
assert alignment.query_begin == 0
assert alignment.query_end == 14
assert alignment.ref_end_next_best == 0
assert alignment.mismatches == 2
assert alignment.cigar_string == "4=1X4=1I5="

Example 5: Print Alignment Result

import mssw

reference = "CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA"
query = "CTGAGCCGGTAAATC"
aligner = mssw.Aligner(match=3, mismatch=1, gap_open=2, gap_extend=2)
alignment = aligner.align(query, reference)
alignment.print()