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Python Package for RNA structure prediction analysis.

Project Description

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.

MANUALS http://multifoldmanual.appspot.com

SOURCES CODES https://pypi.python.org/pypi/multifold

PREREQUISITES 1. python 2.7, python-dev 2. numpy >= 1.4.1 (automatically installed) 3. ngslib >= 1.1.10 for NGS data processing (automatically installed) 4. fisher >= 0.1.4 for fisher exact test ((automatically installed) 4. 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=$HOME/local multifold
  2. Install from source file (including the demo example files) >easy_install –editable –build-directory package_source/ multifold >cd package_source >python setup.py install –prefix=install_path
  3. sfold 2.2
    Download the stand-alone executable from http://sfold.wadsworth.org/License_info.html
    Run configure file
    >cd SFOLD2.2_HOME >./configure
    Test sfold in command line before use:
    >bin/sfold
    If successful, add sfold binary file to system PATH by:
    PATH=$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.
Release History

Release History

This version
History Node

1.2.2

History Node

1.2.1

History Node

1.2.0

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
multifold-1.2.2.tar.gz (594.5 kB) Copy SHA256 Checksum SHA256 Source Dec 11, 2014

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