Skip to main content

Python Package for RNA structurome quantification 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://rsqwiki.appspot.com

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

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=$HOME/local rsq
  2. Install from source file (including the demo example files) >easy_install –editable –build-directory package_source/ rsq >cd package_source >python setup.py install –prefix=install_path
  3. sfold 2.2
    Download the stand-alone executable from http://sfold.wadsworth.org/License_info.html
    Run configure file
    >cd SFOLD2.2_HOME >./configure
    Test sfold in command line before use:
    >bin/sfold
    If successful, add sfold binary file to system PATH by:
    PATH=$PATH:SFOLD2.2_HOME/bin/

MAJOR MODULES

  • Data formats:
    FastD, FastC, FastS and EFastS to represent data used in RSQ.
  • 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 RSQ.
  • 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


Download files

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

Files for rsq, version 2.0.1
Filename, size File type Python version Upload date Hashes
Filename, size rsq-2.0.1.tar.gz (592.6 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page