Modern Cpp binding for complete-striped-smith-watern-library
Project description
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="
Project details
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