teloscore 0.4.0

Telomeric allele scoring tool for output from Telogator2.

TeloScore

A telomeric allele comparison-scoring tool for output from Telogator2.

Installation

TeloScore can be installed from PyPI using the following command:

pip install teloscore

Usage

The following is an example showing how TeloScore is to be used:

teloscore compare ./sample_01_child.tsv ./sample_02_parent_1.tsv ./out.tsv

Note: There are currently two scoring systems: 1 and 2, corresponding to the scoring systems found in the v0.1.x release and the v0.2.x release. The default is 2. You may specify which scoring system you wish to use by passing --scoring #, where # is 1 or 2.

The output matrix can then be plotted using the following command:

teloscore plot ./out.tsv

Input Format

TeloScore's compare subcommand is primarily designed to accept the TSV output file from Telogator2. However, any TSV file with the following columns would work:

• #chr / chr: Chromosome arm
• allele_id: ID for this specific allele (see Telogator2)
• tvr_consensus: Allele TVR consensus sequence, in the Telogator2 base encoding (https://github.com/zstephens/telogator2/blob/main/resources/kmers.tsv)

Output Format

Definition: TVR = telomere variable region

The output is a TSV matrix with the TVR of the first sample (child) across the columns, and those of the second sample (parent) across the rows. Each entry in the matrix is a floating-point number between 0 and 1, representing a custom similarity score between the two TVRs.

Copyright Notice

TeloScore is a telomeric allele comparison-scoring tool for output from Telogator2.

Copyright (C) 2024-2025 McGill University, David Lougheed

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.