Skip to content

Readme.md

Latest commit

 

History

History
100 lines (80 loc) · 2.83 KB

Readme.md

File metadata and controls

100 lines (80 loc) · 2.83 KB

SHAPE Reactivity Comparison Tool

This script compares two RNA SHAPE(-MaP) reactivity profiles provided in .map format (e.g. in vitro vs in cellulo) and identifies regions with significantly different reactivities. The method is described by Smola et al. (In-cell RNA structure probing with SHAPE-MaP. Nature Protocols 2018 13:6, 13, 1181–1195.)

Dependencies

Python packages

The following Python libraries are required:

  • Python ≥ 3.10
  • numpy
  • pandas
  • matplotlib
  • scipy
  • varnaapi (optional, required only if -f option is used)

They can be installed using:

pip install numpy pandas matplotlib scipy varnaapi

External software

VARNA

For RNA secondary structure visualization, the script uses VARNA via the Python interface varnaapi. VARNA must be installed separately as a .jar file The path to the VARNA .jar file must be provided via an environment variable called VARNA_JAR. This needs to be done once, and then the script can be used without specifying the path again. macOS

echo 'export VARNA_JAR=/path/to/VARNAv3-94a.jar' >> ~/.zshrc
source ~/.zshrc

HPC / bashrc

echo 'export VARNA_JAR=/path/to/VARNAv3-94a.jar' >> ~/.bashrc
source ~/.bashrc

You can verify that the variable is set correctly by running:

echo $VARNA_JAR

The -f / --figures option will fail gracefully if VARNA_JAR is not set. VARNA figure generation (-f option) works best for RNAs up to ~200 nt. More information about VARNA: https://varna.lisn.upsaclay.fr

Notes on environment

The script was developed and tested on macOS with the following Python and library versions:

  • Python 3.10.4
  • numpy 2.2.6
  • pandas 2.2.3
  • matplotlib 3.9.2
  • scipy 1.15.3
  • varnaapi 1.0.0

Other operating systems are supported, provided that Java and VARNA are correctly installed Missing SHAPE reactivities must be encoded as -999

Features

  • Smoothing of SHAPE reactivities and standard errors (rolling window = 3 nt)
  • Calculation of:
    • ΔSHAPE (difference in smoothed reactivities)
    • Z-factor–like metric
    • Standardized score (S)
  • Identification of significantly different regions using a sliding window criterion
  • Spearman correlation between two SHAPE profiles
  • Generation of:
    • tab-delimited output files
    • .shape files for VARNA visualization
    • comparison plots
    • optional VARNA structure figures

Input files

Example input files can be found in the examples/input/ directory.

  • SHAPE reactivity files in .map format (4 columns):
    1. nucleotide index
    2. reactivity value (-999 for missing data)
    3. standard error
    4. nucleotide
  • RNA secondary structure in dot-bracket format (for VARNA visualization)

Usage

python shape_diff_weeks.py \
  -v examples/input/cond1.map \
  -c examples/input/cond2.map \
  -d example/input/test.dot \
  -t first \
  -e second \
  -o -s -f