https://github.com/poke1024/pyalign
Fast and Versatile Alignments for Python
https://github.com/poke1024/pyalign
alignment bioinformatics digital-humanities gotoh-algorithm needleman-wunsch-algorithm smith-waterman-algorithm
Last synced: 5 months ago
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Fast and Versatile Alignments for Python
- Host: GitHub
- URL: https://github.com/poke1024/pyalign
- Owner: poke1024
- License: mit
- Created: 2021-06-17T16:29:15.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2023-06-08T06:45:56.000Z (over 2 years ago)
- Last Synced: 2025-09-08T18:40:01.873Z (5 months ago)
- Topics: alignment, bioinformatics, digital-humanities, gotoh-algorithm, needleman-wunsch-algorithm, smith-waterman-algorithm
- Language: C++
- Homepage:
- Size: 563 KB
- Stars: 50
- Watchers: 2
- Forks: 7
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# pyalign
Fast and simple alignments in Python:
Make sure to take a look at "other alignment libraries" below to better understand if this is
the right library for you.
Alignments have been a staple algorithm in bioinformatics for decades now,
but most packages implementing tend to be either easy to use and slow, or
fast but very difficult to use and highly domain specific.
pyalign is a small and hopefully rather versatile Python package that aims to
be fast and easy to use. At its core, it is an optimizer for finding "optimum
correspondences between sequences" (Kruskal, 1983) - the main proponents of which
are alignments and dynamic time warping.
General Features:
* easy to install and easy to use
* robust and efficient implementation of standard algorithms
* very fast for smaller problem sizes (see below for details)
* built-in visualization functionality for teaching purposes
In terms of alignment algorithms:
* computes local, global and semiglobal alignments on pairs of sequences
* supports different gap costs (commonly used ones as well as custom ones)
* automatically selects best suitable algorithm (e.g. Gotoh)
* no assumptions on matched items, i.e. not limited to characters
* supports any given similarity or distance function (i.e. can maximize or minimize)
* can return one as well as *all* optimal alignments and scores
The implementation should be rather fast due to highly optimized code paths
for every special case. While it does *not* support GPUs, here are some facts:
* optimized C++ core employing xtensor
* supports SIMD via batching (i.e. simple SIMD parallelism as first
suggested by Alpern et al. and more recently by Rudnicki et al.)
* carefully designed to avoid dynamic memory allocation
* extensive metaprogramming to provide different optimized code paths for different
usage patterns - for example, computing "only single score" won't write tracebacks,
whereas computing "all alignments" will track multiple traceback edges
# Installation
## via pip (recommended)
pyalign currently provides precompiled packages for Windows (Intel), Linux (Intel)
and macOS (Intel).
`pip install pyalign`
## on Google Colab
First install conda via:
```
!pip install -q condacolab
import condacolab
condacolab.install()
```
Then run:
```
!git clone https://github.com/poke1024/pyalign && cd pyalign && conda env create -f environment.yml && conda activate pyalign && python setup.py install
```
## locally
Installing pyalign locally will require a modern C++ compiler. It also requires
various libraries from the [xtensor stack](https://github.com/xtensor-stack)
which are best installed via cona; for the full list of required packages, see
[environment.yml](environment.yml).
Local installation via conda:
```
git clone https://github.com/poke1024/pyalign
cd pyalign
conda env create -f environment.yml
conda activate pyalign
python setup.py install
```
# Example
Running
```python
import pyalign
alignment = pyalign.global_alignment("INDUSTRY", "INTEREST", gap_cost=0, eq=1, ne=-1)
alignment
```
will compute an optimal global alignment between "INDUSTRY" and "INTEREST".
We instruct the optimizer to use of scores 1 and -1 (for matching and non-matching letters) and no (i.e. 0) gap costs.
In Jupyter, this will give
```
IN----DUSTRY
|| ||
INTERE--ST--
```
Of course you can also extract the actual score:
```python
alignment.score
```
as
```python
4.0
```
It's also possible to extract the traceback matrix and path and generate
visuals (and thus a detailed rationale for the obtained score and solution).
In contrast to the first example above, which used the simplified high level
API, we now use the full, more detailed API, which gives much more detailed
access to different gap costs, solvers and scoring configurations. To make
things a bit more interesting, we switch from 0 gap cost to 0.2 (which will
not change the result in this case, but shows in the traceback matrix):
```python
import pyalign.problems
import pyalign.solve
import pyalign.gaps
pf = pyalign.problems.general(
pyalign.problems.Equality(eq=1, ne=-1),
direction="maximize")
solver = pyalign.solve.GlobalSolver(
gap_cost=pyalign.gaps.LinearGapCost(0.2),
codomain=pyalign.solve.Solution)
problem = pf.new_problem("INDUSTRY", "INTEREST")
solver.solve(problem)
```
As a final example, here is how we would modify the `solver` above to get a list over all optimal
solutions of a problem:
```python
from typing import Iterator
solver = pyalign.solve.GlobalSolver(
gap_cost=pyalign.gaps.LinearGapCost(0.2),
codomain=List[pyalign.solve.Solution])
```
This will now return a list of solutions, each with its own traceback, e.g.:
```python
[,
]
```
To learn more about the API, take a look at
[](https://mybinder.org/v2/gh/poke1024/pyalign-demo/HEAD?filepath=example.ipynb)
# Performance
Here are a few benchmarks. The "pure python" implementation seen in this
benchmark is found at https://github.com/eseraygun/python-alignment.
`+alphabet` means using `pyalign.problems.alphabetic` instead of
the simpler `pyalign.problems.general` to construct a problem.
`+SIMD` means feeding groups of equally-structured aligment problems into
one `solve` call by using `pyalign.problem.ProblemBatch` - doing this will
internally make use of [AVX2](https://en.wikipedia.org/wiki/Advanced_Vector_Extensions)
on Intel and [Neon](https://developer.arm.com/technologies/neon) on ARM processors.
The following benchmarks were done on an Apple M1 Max. SIMD-128 refers to the M1's 128-bit SIMD.
The benchmark code can be found under [benchmark.py](demo/py/benchmark.py).
# Other Alignment Libraries
Here is a short overview of other libraries.
## Nice General Purpose Implementations
* https://github.com/stanfordnlp/string2string (RECOMMENDED!)
* https://pypi.org/project/textdistance/
* https://edist.readthedocs.io/en/latest/
* https://github.com/maxbachmann/RapidFuzz
## For large scale / bioinformatics problems
What you will *not* find in pyalign:
* SIMD acceleration for single pairs of sequences as in e.g. (Farrar 2007)
* GPU acceleration, see e.g. (Barnes, 2020)
* approximate or randomized algorithms
* advanced preprocessing or indexing
If you need any of the above, you might want to take a look at:
* https://pypi.org/project/edlib/
* https://github.com/smarco/WFA2-lib and https://github.com/kcleal/pywfa
* https://github.com/vishnubob/ssw
* https://github.com/lh3/ksw2
* https://github.com/Daniel-Liu-c0deb0t/block-aligner
* https://github.com/jeffdaily/parasail
* https://biopython.org/docs/latest/api/Bio.Align.html
* http://cudasw.sourceforge.net/homepage.htm
* https://blast.ncbi.nlm.nih.gov/Blast.cgi
## Even more alignment libraries
* https://github.com/mbreese/swalign/
* https://github.com/seqan/seqan3
* https://github.com/wannesm/dtaidistance
# References
## Original Works
Altschul, S. (1998). Generalized affine gap costs for protein sequence alignment. Proteins: Structure, 32.
Gotoh, O. (1982). An improved algorithm for matching biological sequences. Journal of Molecular Biology, 162(3), 705–708. https://doi.org/10.1016/0022-2836(82)90398-9
Sankoff, D. (1972). Matching Sequences under Deletion/Insertion Constraints. Proceedings of
the National Academy of Sciences, 69(1), 4–6. https://doi.org/10.1073/pnas.69.1.4
Smith, T. F., & Waterman, M. S. (1981). Identification of common
molecular subsequences. Journal of Molecular Biology, 147(1), 195–197.
https://doi.org/10.1016/0022-2836(81)90087-5
Miller, W., & Myers, E. W. (1988). Sequence comparison with concave weighting functions. Bulletin of Mathematical Biology, 50(2), 97–120. https://doi.org/10.1007/BF02459948
Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable
to the search for similarities in the amino acid sequence of two proteins.
Journal of Molecular Biology, 48(3), 443–453. https://doi.org/10.1016/0022-2836(70)90057-4
Waterman, M. S., Smith, T. F., & Beyer, W. A. (1976). Some biological sequence metrics.
Advances in Mathematics, 20(3), 367–387. https://doi.org/10.1016/0001-8708(76)90202-4
Waterman, M. S. (1984). Efficient sequence alignment algorithms. Journal of Theoretical Biology, 108(3), 333–337. https://doi.org/10.1016/S0022-5193(84)80037-5
## Other Algorithms
Chakraborty, A., & Bandyopadhyay, S. (2013). FOGSAA: Fast Optimal Global Sequence Alignment Algorithm. Scientific Reports, 3(1), 1746. https://doi.org/10.1038/srep01746
## Surveys
Aluru, S. (Ed.). (2005). Handbook of Computational Molecular Biology.
Chapman and Hall/CRC. https://doi.org/10.1201/9781420036275
Stojmirović, A., & Yu, Y.-K. (2009). Geometric Aspects of Biological Sequence Comparison. Journal of Computational Biology, 16(4), 579–610. https://doi.org/10.1089/cmb.2008.0100
Kruskal, J. B. (1983). An Overview of Sequence Comparison: Time Warps,
String Edits, and Macromolecules. SIAM Review, 25(2), 201–237. https://doi.org/10.1137/1025045
Müller, M. (2007). Information Retrieval for Music and Motion. Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-540-74048-3
## Implementations
Alpern, B., Carter, L., & Su Gatlin, K. (1995). Microparallelism and high-performance protein matching. Proceedings of the 1995 ACM/IEEE Conference on Supercomputing (CDROM) - Supercomputing ’95, 24-es. https://doi.org/10.1145/224170.224222
Barnes, R. (2020). A Review of the Smith-Waterman GPU Landscape. https://www2.eecs.berkeley.edu/Pubs/TechRpts/2020/EECS-2020-152.html
Farrar, M. (2007). Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics, 23(2), 156–161. https://doi.org/10.1093/bioinformatics/btl582
Flouri, T., Kobert, K., Rognes, T., & Stamatakis, A. (2015). Are all global alignment algorithms and implementations correct? [Preprint]. Bioinformatics. https://doi.org/10.1101/031500
Rognes, T. (2011). Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinformatics, 12(1), 221. https://doi.org/10.1186/1471-2105-12-221
Rudnicki, W. R., Jankowski, A., Modzelewski, A., Piotrowski, A., & Zadrożny, A. (2009). The new SIMD Implementation of the Smith-Waterman Algorithm on Cell Microprocessor. Fundamenta Informaticae, 96(1–2), 181–194. https://doi.org/10.3233/FI-2009-173
Tran, T. T., Liu, Y., & Schmidt, B. (2016). Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi. 26th International Symposium on Computer Architecture and High Performance Computing, 54, 128–138. https://doi.org/10.1016/j.parco.2015.11.001