tn93 1.0.1

A python implementation of the Tamura-Nei distance for HIV sequences

Tamura-Nei Distance Calculation with Python

Overview

This repository contains a Python implementation of the Tamura-Nei (TN93) distance calculation for HIV sequences. When provided with two HIV sequences to compare, this software returns a distance value between 0 and 1. See NOTES for more information on the algorithm

Usage

This tool is primarily meant as a library to be imported and used in custom analysis code, but can also be used to directly calculate the pairwise distances for a set of sequences in a FASTA file.

First, install using pip

pip install tn93

or clone this respository and copy src/tn93.py to your working directory. To calculate the distance between a pair of sequences,

from Bio import SeqIO
import tn93
# Read in a FASTA file to get sequences
seqs = [ x for x in SeqIo.parse("your_sequences.fasta", format="fasta") ]
tn93 = tn93.TN93()
distance = tn93.tn93_distance(seqs[0], seqs[1], "RESOLVE")

Alternatively, the module can be run from the command line and provided with a sequence file and match mode to produce a JSON file with the pairwise distances.

python tn93.py --input_file example_seqs.fasta --match_mode RESOLVE --output example_seqs_resolve_distance.json

There are four distinct match modes:

• SKIP, which ignores ambiguous positions
• GAPMM, which treats gaps appearing in only one sequence as mismatches
• RESOLVE, which tries to resolve the ambiguity to a single nucleotide, averages if that fails
• AVERAGE, which takes the average of the possible resolution values

Related documents

• Open Practices
• Rules of Behavior
• Thanks and Acknowledgements
• Disclaimer
• Contribution Notice
• Code of Conduct

Public Domain Standard Notice

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License Standard Notice

The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.

This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

This source code in this repository 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 Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

The source code forked from other open source projects will inherit its license.

Privacy Standard Notice

This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/other/privacy.html.

Contributing Standard Notice

Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.

Records Management Standard Notice

This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.

Additional Standard Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.