Skip to main content
Help us improve PyPI by participating in user testing. All experience levels needed!

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.

Project details


Release history Release notifications

This version
History Node

1.2.2

History Node

1.2.1

History Node

1.2.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
multifold-1.2.2.tar.gz (594.5 kB) Copy SHA256 hash SHA256 Source None Dec 11, 2014

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page