cdr3-parser

A simple program to convert aafreq files (generated as an intermediate step from ATTILA) into csv or json files containing statistics about all VH-CDR3 regions presented in the input file.

Overview

$ cdr3-parser --help

cdr3-parser 0.1.0
Output chemical properties and statistics of CDR3 sequences within a `aafreq` file.
You may choose either `json` or `csv` as output formats.

USAGE:
    cdr3-parser [FLAGS] <INPUT_FILE>

FLAGS:
        --cdr-only    Informs program that the input contains only CDR3VH sequences, separated by a new line
    -c, --csv         Select `csv` as output format [default]
    -h, --help        Prints help information
    -j, --json        Select `json` as output format
    -V, --version     Prints version information

ARGS:
    <INPUT_FILE>    Sets the input file to use

Installation

The project is still in 'alpha', only intended for local use at the University of Brasília's Bioinformatics Laboratory, but if you want to run it locally, you can compile the source code. Just bear in mind that you'll need a working rust installation in order to do that.

git clone https://github.com/Cardosaum/cdr3-parser.git
cd cdr3-parser
cargo install --path .

After successfully compiling the code, and assuring that ~/.cargo/bin is in your $PATH, you are good to go :)