DVQ - DNA Visualisations and Quick comparisons
Abstract We introduce DVQ (DNA Visualisations and Quick comparisons), an open-source Python library for exploring nucleotide sequences using a variety of methods. Understanding DNA sequences intuitively is important for a variety of tasks in biology. DVQ aims to be a one-stop comprehensive library that makes explainable DNA easy for geneticists, researchers, and practitioners who need explanations. For practitioners, the library provides an easy-to-use interface to generate visualisations for their sequences by only writing a few lines of code. In this report, we demonstrate several example use cases across different types of sequences as well as visualisations.
Simple early version preprint: http://dx.doi.org/10.13140/RG.2.2.19227.89125
Methods Implemented:
Visual
- Persistant Homological Representations
- ColorSquare
- C-Curve - Removed from development plan due it being redundant vs a 2D Line
- Spider Representation - Removed from development plan due to it being found to be difficult to use for large sequences
- 2D Line
- Chaos Game Representation
Statistical
- Deng entropy
- KL Divergence plain, computes distros of chunks similar to deng entropy.
- KL Divergence KL div like measure using deng entropy.
- KL Divergence
- Perpelxity
- Entropy
- K-Mer overlap
- fast K-Mer overlap, (current implementation is too slow or stuck)
- Wen's Method
- JS Divergence
- Wasserstein Distance
Overview:
- How to use dvq
from dvq import visual
visual.plot_2d_comparison([seqs_1, seqs_2], ['seq_1', 'seq_2'])
from dvq import statistical
statistical.similarity_wen([seqs_1, seqs_2])
# 0.99
1 maintainer
Metadata
1 maintainer
Release files for dvq 0.0.4.8.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| dvq-0.0.4.8.5.tar.gz | 13.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| dvq-0.0.4.8.5-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 26.6 kB
Release files / dvq-0.0.4.8.5.tar.gz
| Download URL | dvq-0.0.4.8.5.tar.gz |
|---|---|
| Size | 13.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
297abce79fbe59267f7e7bc4020da02cdac78019106ebfdf50cdab4478536cdd
|
|
BLAKE2b-256 checksum How to use checksums |
8d560f8a252f71a23590fd45a2bc46730d28cffbd03b2213c59437a87a7630bd
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.11.11
|
Release files / dvq-0.0.4.8.5-py3-none-any.whl
| Download URL | dvq-0.0.4.8.5-py3-none-any.whl |
|---|---|
| Size | 13.3 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
2637232bb48cf93bb769c50dd8b423a19855f1fab26b4c27230b9971af8363e3
|
|
BLAKE2b-256 checksum How to use checksums |
c21a344d58d871a56716b1907e84bd6701d5fa93ce62f95921e86b85d8b631bf
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.11.11
|
