mutalyzer-algebra
=================
A Boolean Algebra for Genetic Variants
A set of Boolean relations: equivalence; containment, i.e., either a
variant is fully contained in another or a variant fully contains another;
overlap, i.e., two variants have (at least) one common element; and
disjoint, i.e., no common elements that allows for a comprehensive
classification of the relation for every pair of variants by taking all
minimal Longest Common Subsequence (LCS) alignments into account.
[Jonathan K. Vis, Mark A. Santcroos, Walter A. Kosters and Jeroen F.J. Laros.
"A Boolean Algebra for Genetic Variants." In: *Bioinformatics* (2023).](https://doi.org/10.1093/bioinformatics/btad001)
Installation
------------
Use pip to install from the Python Package Index (PyPI).
```bash
python -m pip install mutalyzer-algebra
```
Or directly from GitHub for development (after cloning in an active
virtual environment).
```bash
python -m pip install --upgrade --editable .[dev]
```
Testing
-------
Run the tests.
```bash
python -m coverage run
```
Usage
-----
Use the command-line interface.
```bash
algebra --reference "AAAAA" compare --lhs-hgvs "1_2insTA" --rhs-hgvs "2_3insT"
```
Or as a Python package.
```python
from algebra import compare
from algebra.variants import parse_hgvs
reference = "AAAAA"
lhs = parse_hgvs("1_2insTA")
rhs = parse_hgvs("2_3insT")
# returns: Relation.DISJOINT
compare(reference, lhs, rhs)
reference = "CATATATC"
lhs = parse_hgvs("2_7AT[4]") # observed: CATATATATC
rhs = parse_hgvs("5_6insT") # observed: CATATTATC
# returns: Relation.CONTAINS
compare(reference, lhs, rhs)
```
Extracting variants from sequences.
```python
from algebra.extractor import extract_sequence, to_hgvs
reference = "CATATATC"
observed = "CATATATATC"
canonical, _ = extract_sequence(reference, observed)
# returns: 2_7AT[4]
to_hgvs(canonical, reference)
```
Variant normalization.
```python
from algebra.extractor import extract, to_hgvs
from algebra.variants import parse_hgvs
reference = "CATATATC"
variant = parse_hgvs("6_7dupAT")
canonical, _ = extract(reference, variant)
# returns: 2_7AT[4]
to_hgvs(canonical, reference)
```
See Also
--------
A web interface with integration with [Mutalyzer](https://github.com/mutalyzer): [Mutalyzer Algebra](https://mutalyzer.nl/algebra)
[Mutalyzer Algebra on PyPI](https://pypi.org/project/mutalyzer-algebra/)
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