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.

Usage: aadiff [OPTIONS]

Options:
  -i, --input-fasta <INPUT_FASTA>
          Optional input fasta
  -o, --output-tsv <OUTPUT_XSV>
          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 <OUTPUT_DELIMITER>
          Use the provider delimiter for separating fields. Default is ','
  -h, --help
          Print help

Build

We provide downloads in the release page.

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:

,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.

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