Metadata-Version: 2.1
Name: dvq
Version: 0.0.4.7.0
Summary: This is a library to validate and compare dna sequences
License: Apache-2.0
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: persim
Requires-Dist: ripser
Requires-Dist: Cython
Provides-Extra: test
Requires-Dist: pytest; extra == "test"

# DVQ - DNA Validations and Quick comparisons 
A package with some useful functions to compare DNA sequences both visually and statistically. 

## Methods:
- [x] [Persistant Homological Representations](https://american-cse.org/csci2022-ieee/pdfs/CSCI2022-2lPzsUSRQukMlxf8K2x89I/202800b599/202800b599.pdf)
- [x] [ColorSquare](https://match.pmf.kg.ac.rs/electronic_versions/Match68/n2/match68n2_621-637.pdf)
- [x] [C-Curve](https://pubmed.ncbi.nlm.nih.gov/23246806/) - Removed from development plan due it being redundant vs a 2D Line
- [x] [Spider Representation](https://www.researchgate.net/publication/260971259_Spider_Representation_of_DNA_Sequences) - Removed from development plan due to it being found to be difficult to use for large sequences
- [ ] [KL Divergence](https://pubmed.ncbi.nlm.nih.gov/31981184/)
- [ ] [Perpelxity](https://arxiv.org/pdf/1202.2518.pdf)
- [ ] [Entropy](https://pubmed.ncbi.nlm.nih.gov/9344742/)
- [x] [2D Line](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC162336/)
- [x] K-Mer overlap
- [x] [Wen's Method](https://pubmed.ncbi.nlm.nih.gov/29765099/)

## Overview:

* How to use dvq
```python
from dvq import visual

visual.plot_2d_comparison([seqs_1, seqs_2], ['seq_1', 'seq_2'])

```

![An example graphic comparing sequences ](Untitled.png "2D Comparison - Same virus")
