STRUCT (previously named as SPLASH-structure)

This repository contains the official implementation accompanying our manuscript: STRUCT: a statistical approach to identify RNA secondary structures from raw sequencing data, bypassing multiple sequence alignment. Read the paper on bioRxiv.

Setting up the Python Environment

It is recommended to use a virtual environment to manage dependencies. Ensure you have Python >= 3.9 installed. Then, follow these steps:

# Create a virtual environment (you can replace 'my_env' with any name)
python3 -m venv my_env

# Activate the virtual environment
source my_env/bin/activate

Installing STRUCT

You can install STRUCT by cloning the repository and using pip to install the package and its dependencies:

# Clone the repository
git clone https://github.com/juliefrwang/splash-structure.git

# Navigate to the project directory
cd splash-structure

# Install the package
pip install .

Installing Julia programming language

STRUCT relies on Julia for some computations. Follow the steps below to install Julia and set up the required packages.

Installing Julia

You can download and install Julia from the official website: https://julialang.org/downloads/. After installing, verify your Julia installation:

julia --version

Installing Julia Packages

Install the required Julia packages for this project, run:

julia -e 'using Pkg; Pkg.add("DataFrames"); Pkg.add("CSV"); Pkg.add("Combinatorics")'

Usage

After installation, you can run STRUCT directly from the command line. STRUCT provides two handy commands: ss-target for executing target mode and ss-compactor for running compactor mode.

Target mode syntax:

ss-target <splash_output_file> <output_prefix>

Positional Arguments

1. <splash_output_file>: Path to the SPLASH output file. For SPLASH, please see: https://github.com/refresh-bio/SPLASH.
2. <output_prefix>: Prefix for naming the output result folder.

Compactor mode syntax:

ss-compactor <compactor_file> <output_prefix>

Positional Arguments

1. <compactor_file>:Path to the compactor file.
2. <output_prefix>: Prefix for naming the output result folder.

Example runs on test data

There are two files in tests/test_data/: test.after_correction.scores.tsv, a test SPLASH output file, and test_compactor.tsv, a test compactor file. To run STRUCT from splash-structure folder with an output folder prefix new_test:

Run target mode

ss-target new_test tests/test_data/test.after_correction.scores.tsv

Run compactor mode

ss-compactor new_test tests/test_data/test.compactor.tsv

The output will be saved in the new_test_results folder. The file structure_on_targets.tsv contains the target mode results, and structure_on_compactors.tsv contains the compactor mode results. The subfolder interm_compactor contains an intermediate file for processed compactors before the algorithm searches for compensatory stems.