ShapeCompare is a free software for GNU/linux, Mac OS and Windows made to visualise and compare results of high-throughput Selective 2′-Hydroxyl Acylation analysed Primer Extension (hSHAPE) experiments.
Align and display multiple hSHAPE experiments. The color of each base is related to its flexibility. (Blue = low reactivity, Red = high reactivity, Grey : No data)
Plot reactivity of each base in sequence order. Errorbar are standard deviations.python cli.py scatter data/experiment.shape data/experiment2.shape
Plot reactivity of each base in decreasing order. Errorbar are standard deviations.
Plot reactivity over a secondary structure model. Paired bases are in bold.
Format file for model consist in two csv files begining with the same name.
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)
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.)
-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.
ShapeCompare is written in python 2.7 and needs the following library :
How to get ShapeCompare to play nice with your data ? Follow this steps :
Page of the older GUI version (11 March 2013) : ShapeCompare 0.3.x
This program has been written by Guilhem Doulcier, originally during a two week internship in the Institut de Biologie de l' École normale supérieure in november 2012.
Copyright (C) 2012, 2013 Guilhem DOULCIER.
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.