Python-version of SwiSpot

Download:
Python-cmdline-SwiSpot-0.2.2.tar.gz.

Python Dependencies

Required Modules:

  • Numpy
  • Scikit-learn
  • ViennaRNA python wrapper [Will be installed with ViennaRNA]

    Non-Python Dependencies

    An installed version of ViennaRNA [Tested with ViennaRNA 2.1.9, it could work with newer versions] is required. For the current version of ViennaRNA python interface is compiled and installed by default. ViennaRNA can be downloaded from Vienna TBI and installed following the instructions.

    tar -zxvf ViennaRNA-2.1.9.tar.gz
    cd ViennaRNA-2.1.9
    ./configure
    make

    optional

    sudo make install

    Mac OS X user can install ViennaRNA using homebrew:

    brew install ViennaRNA


    • Installation

    SwiSpot can be easily installed using the provided setup.py. The required libraries will be installed by the package. An installed and linked ViennaRNA with python wrapper is needed!

    Unpack cmdline-SwiSpot-x.y.z.tar.gz

    tar -zxvf cmdline-SwiSpot-x.y.z.tar.gz

    Enter directory

    cd cmdline-SwiSpot-x.y.z

    Install:

    python setup.py install


    Usage

     
SwiSpot [-h] [-c CONF] [-d {bp,md}] [-p] [-s {standard,wider}]
             [-t TEMPERATURE] [-o OUTPUT] [--pattern PATTERN]
             [--shinedalgarno SHINEDALGARNO] [-f {png,eps,jpeg}]
             [--version] [--verbosity]                  
			 sequence

             positional arguments:
               sequence              Sequence to be evaluated using the program

             optional arguments:
               -h, --help            show this help message and exit
               -c CONF, --conf CONF  Provide a path for the conf file
               -d {bp,md}, --distance {bp,md}
                                     Distance function for clustering
               -p, --probability     Uses probability matrix insted of sampled ensemble for
                                     switching sequence spvotting
               -s {standard,wider}, --sampling {standard,wider}
                                     Select between standard sampling, at fixed temperature
                                     T, and wider sampling
               -t TEMPERATURE, --temperature TEMPERATURE
                                     Sampling temperature
               -o OUTPUT, --output OUTPUT
                                     output data file
               --pattern PATTERN     Provide a path for the pattern file, default pattern
                                     are ({3,}[ACGT]{3,8}){3,}.T{3,}.{,30}$ and
                                     ){8,}T{3,}.{,30}$
               --shinedalgarno SHINEDALGARNO
                                     Provide a path for the SD sequences file.
               -f {png,eps,jpeg}, --figures {png,eps,jpeg}
                                     Plot figures with varna
               --version             show program's version number and exit
               --verbosity           increase output verbosity


    Pattern file and Shine-Dalgarno sequences file

    Users can provide their own pattern for terminator hairpins, using --pattern FILEPATH (a plain text file one for each row, see pattern.txt for an example). Moreover users can provide their own Shine-Dalgarno sequences via a plain text file, using the command --shinedalgarno FILEPATH, (shine-dalgarno.txt for an example.)