{ "info": { "author": "Yunfei Wang", "author_email": "yfwang0405@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Developers", "License :: Free for non-commercial use", "License :: OSI Approved :: GNU General Public License (GPL)", "Operating System :: Unix", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "CONTENTS AND COPYRIGHT\r\n\r\nThis 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.\r\n\r\nMANUALS\r\nhttp://multifoldmanual.appspot.com\r\n\r\nSOURCES CODES\r\nhttps://pypi.python.org/pypi/multifold\r\n\r\nPREREQUISITES\r\n1. python 2.7, python-dev\r\n2. numpy >= 1.4.1 (automatically installed)\r\n3. ngslib >= 1.1.10 for NGS data processing (automatically installed)\r\n4. fisher >= 0.1.4 for fisher exact test ((automatically installed)\r\n4. sfold 2.2 stand-alone executable (http://sfold.wadsworth.org/License_info.html)\r\n\r\nGENERAL INSTALL INSTRUCTIONS\r\n\r\n1. Install from Python Package Index (https://pypi.python.org)\r\n > easy_install --prefix=$HOME/local multifold\r\n\r\n2. Install from source file (including the demo example files)\r\n >easy_install --editable --build-directory package_source/ multifold\r\n >cd package_source\r\n >python setup.py install --prefix=install_path\r\n\r\n3. sfold 2.2\r\n Download the stand-alone executable from http://sfold.wadsworth.org/License_info.html\r\n\tRun configure file\r\n\t >cd SFOLD2.2_HOME\r\n\t >./configure\r\n\tTest sfold in command line before use:\r\n\t >bin/sfold\r\n\tIf successful, add sfold binary file to system PATH by:\r\n\t PATH=$PATH:SFOLD2.2_HOME/bin/\r\n\r\nMAJOR MODULES\r\n\r\n- Data formats:\r\n\tFastD, FastC, FastS and EFastS to represent data used in MultiFold.\r\n\r\n- IO:\r\n\tReaders for each data format\r\n\r\n- Predictor:\r\n\tWrappers of a series of RNA secondary structure prediction tools.\r\n\tRNAfold, mfold, UNAFold, sfold, et. al.\r\n\tNote: make sure the command/program is callable in shell before call it in MultiFold.\r\n\r\n- Algorithm:\t\r\n\tEM algoritm, Boltzmann sampling, structure distance calculation, et. al.\r\n\r\n- Utils: \r\n Utilites. 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