Utitilies for constructing and manipulating models for non-local structural dependencies in genomic sequences
Infer non-local structural dependencies in genomic sequences. Genomic sequences are esentially compressed encodings of phenotypic information. This package provides a novel set of tools to extract long-range structural dependencies in genotypic data that define the phenotypic outcomes. The key capabilities implemented here are as follows:
- Compute the Quasinet (Q-net) given a database of nucleic acid sequences. The Q-net is a family of conditional inference trees that capture the predictability of each nucleotide position given the rest of the genome. The constructed Q-net for COVID-19 and Influenza A H1N1 HA 2008-9 is shown below.
Compute a structure-aware evolution-adaptive notion of distance between genomes, which is demonstrably more biologically relevant compared to the standard edit distance.
Draw samples in-silico that have a high probability of being biologically correct. For example, given a database of Influenza sequences, we can generate a new genomic sequence that has a high probability of being a valid influenza sequence.
To install with pip:
pip install quasinet
NOTE: If trying to reproduce the paper below, please use
pip install quasinet==0.0.58
from quasinet import qnet # initialize qnet myqnet = qnet.Qnet() # train the qnet myqnet.fit(X) # compute qdistance qdist = qnet.qdistance(seq1, seq2, myqnet, myqnet)
Examples are located here.
For more documentation, see here.
For reference, please check out our paper:
You can reach the ZED lab at: zed.uchicago.edu
Release history Release notifications | RSS feed
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size||File type||Python version||Upload date||Hashes|
|Filename, size quasinet-0.0.87-py3-none-any.whl (15.1 MB)||File type Wheel||Python version py3||Upload date||Hashes View|
|Filename, size quasinet-0.0.87.tar.gz (14.4 MB)||File type Source||Python version None||Upload date||Hashes View|
Hashes for quasinet-0.0.87-py3-none-any.whl