AA Diff

Produces simple amino acid difference tables.

Usage

If -i is not specified, the program will use (and block on) STDIN. If -o is not specified, the program will write to STDOUT.

```bash Usage: aadiff [OPTIONS]

Options: -i, --input-fasta Optional input fasta -o, --output-tsv Optional output delimited file -r, --restrict-to-pairwise-alignable Restrict to non-ambiguous alignable regions, pairwise -e, --unix-line-endings Use unix line-endings instead of Windows ones -d, --output-delimiter Use the provider delimiter for separating fields. Default is ',' -h, --help Print help ```

Build

We provide downloads in the release page.

```bash rustup toolchain install nightly \ git clone https://github.com/CDCgov/aadiff cd aadiff cargo +nightly b -r

Install here:

ls -l target/release/aadiff* ```

Algorithm Description

Requirements

• The first sequence is used as the reference
• Takes aligned DNA sequences in valid IUPAC (otherwise it will get recoded)
• Optionally: only alignable portions can be compared, e.g., the range containing the first and last non-ambiguous amino acid residue.

Disambiguation of degenerate codons

• The Reference is not disambiguated
• We only report up to 3 ambiguous translations for degenerate codons (changed from the legacy implementation)

TODO

• Should we scrub delimiters from strain names? Otherwise we could fail.
• Provide JSON output

Output

The default output produces:

csv ,A/ref/strain/20XX,A/query1/strain/20XX,A/query2/strain/20XX,A/query3/strain/20XX 142,N,,,"S", 155,I,"V","R","V" 181,S,"P",,, 185,A,,"G","T","G", 201,I,,"V","S","V", 210,V,"A",,, 218,K,"E/K",,, 230,F,"Y",,, 270,V,"L",,,"del"

Is equivalent to:

| Position | A/ref/strain/20XX | A/query1/strain/20XX | A/query2/strain/20XX | A/query3/strain/20XX | | -------- | ----------------- | -------------------- | -------------------- | -------------------- | | 142 | N | | S | | | 155 | I | V | R | V | | 181 | S | P | | | | 185 | A | | G | T/G | | 201 | I | | V | S/V | | 210 | V | A | | | | 218 | K | E/K | | | | 230 | F | Y | | | | 270 | V | L | | del |

Acknowledgements

This work ports some functionality created by James Smagala originally written in Python.

Notices

Contact Info

For direct correspondence on the project, feel free to contact: Samuel S. Shepard, Centers for Disease Control and Prevention.

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. 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.