This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
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/
export PATH

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 threading processing procedures.

EXAMPLES

Examples are in the examples folder.
1. Dealing with genes without isoforms.
2. Dealing with genes with multiple isoforms.
3. Advanced usage in tuning parameters and adding in external input.
Release History

Release History

2.0.2

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

2.0.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

2.0.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
rsq-2.0.2.tar.gz (594.7 kB) Copy SHA256 Checksum SHA256 Source Mar 19, 2015

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS HPE HPE Development Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting