install

CONTENTS AND COPYRIGHT

This package is used for manipulating genome annotation and sequence files, such as Bed, GenePred, BAM,
Wiggle and BigWig formats. Users interested in this package should contact yfwang0405ATgmail.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 yfwang0405ATgmail.com.

PREREQUISITES

1. python 2.6 or 2.7
2. numpy >=1.4.1 (automatically installed)
3. fisher >=0.1.4 (automatically installed)
4. argparse if Python version is2.6 (automatically installed)
5. ngslib >= 1.1.10 for NGS data processing (automatically installed)
6. 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

>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
>./configure

• Test sfold in command line before use:

>bin/sfold

• If successful, add sfold binary file to system PATH by:

PATH=$PATH:$HOME/software/sfold2.2/bin/ # replace with the real path
export PATH

4. Testing

• Test if rsq works:

>rsq

• It will shows:

Program: rsq 1.2.0 (Python Package for RNA structurome quantification
using RNA structure profiling data.)

optional arguments:
  -h, --help  show this help message and exit

Sub commands:
  FastD       FastD file utilities.
  FastC       FastC file utilities.
  fold        Fold RNA structures.
  FastS       FastS utilities.
  isoform     Deal with isoform cases.
  quantify    Quantification of RNA structures.
  draw        Draw RNA secondary structures.
  fitness     Fitness between sequencing depth (FastD) and structure (FastS).

dependency rsq, ngslib

INSTALL OPTIONAL RNA PREDICTION TOOLS

• RSQ has wrappers for a series of commonly used RNA structure prediction tools, including RNAfold, mfold, UNAFold, RNAStructure, ipknot et. al.
• Users have to install any ones they like to call them in RSQ package.

# test if the binary is installed in shell
> RNAfold

Output:

Input string (upper or lower case); @ to quit
....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8

• The wrappers have uniform interfaces, accept FastC as input and FastS as output.

fs = RSQ.Predictors.RNAfold(fc,37.0) # fc is FastC input, 37 is folding temperature

• Users can call multiple prediction tools with MergeFold function. The output will be merged.

fs = RSQ.Predictors.MergeFold(fc,37.,0,['RNAfold','RNAStructure','mfold'])