Trainable RNA Structural Aligner

Installation

This project is written mainly in Rust, a systems programming language. You need to install Rust components, i.e., rustc (the Rust compiler), cargo (the Rust package manager), and the Rust standard library. Visit the Rust website to see more about Rust. You can install Rust components with the following one line:

$ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

The above installation is done by Rustup, and Rustup enables to easily switch a compiler in use. You can install ConsAlign as follows:

$ # AVX, SSE, and MMX enabled for rustc (another example: RUSTFLAGS='--emit asm -C target-feature=+avx2 -C target-feature=+ssse3 -C target-feature=+mmx -C target-feature=+fma')
$ RUSTFLAGS='--emit asm -C target-feature=+avx -C target-feature=+ssse3 -C target-feature=+mmx' cargo install consalign

Check if you have installed ConsAlign properly as follows:

$ consalign # Its available command options will be displayed.

Train ConsAlign Using Your Training Data

To train ConsAlign, you need to install ConsTrain, a training tool of ConsProb (ConsAlign's back engine):

$ git clone https://github.com/heartsh/consprob-trained && cd consprob-trained
$ RUSTFLAGS='--emit asm -C target-feature=+avx -C target-feature=+ssse3 -C target-feature=+mmx' cargo install --path . -f

You can pass ConsTrain your training data as follows:

$ cd scripts
$ # Your trained parameters will appear at "../src/trained_feature_score_sets.rs".
$ constrain -i train_data_dir_path -o train_log_file_path

Now, you can install ConsAlign with your trained parameters:

$ cd ../..
$ git clone https://github.com/heartsh/consalign && cd consalign
$ # Before executing the below command, replace 'consprob-trained = "X.Y"' with 'consprob-trained = {path = "../consprob-trained"}' in "./Cargo.toml" to designate your trained parameters
$ RUSTFLAGS='--emit asm -C target-feature=+avx -C target-feature=+ssse3 -C target-feature=+mmx' cargo install --path . -f
$ # ConsAlign parameterized with your trained parameters will be called
$ consalign

Author

Heartsh

License

Copyright (c) 2018 Heartsh
Licensed under the MIT license.