rsq 2.0.2

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.