Hansel

A graph-inspired data structure for determining likely chains of ordered symbols from breadcrumbs of evidence. Brother of Gretel.

What is it?

Hansel is a probabilistically-weighted, graph-inspired, novel data structure. Hansel is designed to store the number of observed occurrences of a symbol a appearing at some position in space or time i, co-occurring with another symbol b at another position in space or time j.

One may traverse along ordered positions in time or space, each time predicting the next most likely symbol of the sequence to traverse to, given the previously selected symbols in the path. Hansel presents a user-friendly API for managing and interacting with the data stored within.

Requirements

pip install numpy

Install

pip install hanselx

Citation

@article{10.1093/bioinformatics/btaa977,
    author = {Nicholls, Samuel M and Aubrey, Wayne and De Grave, Kurt and Schietgat, Leander and Creevey, Christopher J and Clare, Amanda},
    title = "{On the complexity of haplotyping a microbial community}",
    journal = {Bioinformatics},
    volume = {37},
    number = {10},
    pages = {1360-1366},
    year = {2021},
    month = {01},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btaa977},
    url = {https://doi.org/10.1093/bioinformatics/btaa977},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/37/10/1360/38663805/btaa977.pdf},
}

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License

Hansel and Gretel are distributed under the MIT license, see LICENSE.