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Python Package for RNA structure prediction analysis.

Project description

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CONTENTS AND COPYRIGHT

This package is used for maniputating genome annotation and seqeunce files, such as Bed, GenePred, BAM, Wiggle and BigWig formats. Users interested in this package should contact yfwang0405@gmail.com for details. This package uses the Vienna RNA Package lib and H directories (external/RNAlib/fold) and RNAStructure libs (external/RNAlib/plot), and users should read the COPYING or ReadMe.txt files inside and behave accordingly. All files are copyrighted, but license is hereby granted for personal, academic and non-profit use. Commercial users should contact yfwang0405@gmail.com.

PREREQUISITES
1. python 2.6 or 2.7
2. numpy and scipy (automatically install)
3. scikit-learn for k-means clustering (automatically install)
4. argparse for Python 2.6 (automatically install)
5. ngslib for NGS data processing (automatically install)
6. sfold 2.2 stand-alone executable (http://sfold.wadsworth.org/License_info.html)

GENERAL INSTALL INSTRUCTIONS

1. Install from Python Package Index (https://pypi.python.org)
> easy_install --prefix=$HOME/local multifold

2. Install from source file
>easy_install --editable --build-directory package_source/ multifold
>cd package_source
>python setup.py install --prefix=install_path

3. sfold 2.2
Download the stand-alone executable from http://sfold.wadsworth.org/License_info.html
Run configure file
>cd SFOLD2.2_HOME
>./configure
Test sfold in command line before use:
>bin/sfold
If successful, add sfold binary file to system PATH by:
PATH=$PATH:SFOLD2.2_HOME/bin/

MAJOR MODULES

- Data formats:
FastD, FastC, FastS and EFastS to represent data used in MultiFold.

- IO:
Readers for each data format

- Predictor:
Wrappers of a series of RNA secondary structure prediction tools.
RNAfold, mfold, UNAFold, sfold, et. al.
Note: make sure the command/program is callable in shell before call it in MultiFold.

- Algorithm:
EM algoritm, Boltzmann sampling, structure distance calculation, et. al.

- Utils:
Utilites. Temperature conversion, structure format conversion, et. al.

- ThreadSafeFile:
Used in multiple processing procedures.

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