ShapeCompare

A tool to visualize and compare multiple SHAPE experiment data.

Copyright (C) 2012, 2013 Guilhem DOULCIER

ShapeCompare is a free software for GNU/Linux, Mac OS and Windows made to visualize and compare results of high-throughput Selective 2′-Hydroxyl Acylation analyzed Primer Extension (hSHAPE) experiments.

Features

See http://www.eleves.ens.fr/home/doulcier/shapecompare/ for an overview.

Usage

    cli.py sequences <folders>...  [-v | -o <path>]
    cli.py (histo|scatter) <folders>...  [--rna <seq_name> | -v | -o <path>]
    cli.py twod <folders>...  --model <model_name> [--rna <seq_name> | -v | -o <path>]
    cli.py (-i|--interactive) <folders>...   [-v] 
    cli.py (-h | --help)
    cli.py --version
    cli.py --license

    Commands:
      sequence <folders>...  Align on a sequence multiple experiments.
      histo <folders>...     Bar-plot of reactivity (sequence order).
      scatter <folders>...   Scatter plot of mean reactivity (sorted).
      twod <folders>...      Mean reactivity on a secondary structure template.

    Nb. <folders>... can either be ".shape" folder(s) or folder(s) containing them.
    (In the last case all .shape sub-folders will be evaluated.)

    Options:
    -v --verbose             Execute in verbose mode.
    -i --interactive         Execute in interactive mode. (Not implemented yet).
    -o --output-file <path>  Save the plot in a file instead of displaying it.
    --rna <seq_name>         RNA sequence to show (must be in the fasta file).
    --model <model_name>     Model of secondary structure to use.
    -h --help                Show this screen.
    --version                Show version.
    --license                Show license information.

Example

All experiments in the data_coreset folder: python cli.py histo ../data/shape/data_coreset/ -v

One file only: ./cli.py ../data/shape/data_coreset/7SKWT_RTH_MC5_fit.shape/

How To

How to get ShapeCompare to play nice with your data ? Follow this steps :

1. Get the the code
2. Construct the files corresponding to your favorite RNA : you will need a fasta file with the sequences, and an other with the alignment. (Inspire you from the one I've made for 7SK to get started)
3. Modify the options.py file accordingly.
4. Your data should be in aligned ShapeFinder format (*.shape folder with procTrace.aln inside). If the sequence is different from the first of the fasta file (e.g. mutant) put a seq.txt file inside containing the sequence name to match.
5. Enjoy ! (Don't forget the --help option).

Options

You can modify several aspect of shapeCompare behavior by editing the options.py file.

Requirement

ShapeCompare is written in python 2.7 and needs the following library :

• Numpy and Scipy
• Matplotlib
• Docopt (Included)

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.