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Source code for LOCALIZER

The source code for running LOCALIZER locally can be found here: LOCALIZER_1.0.tar.gz

LOCALIZER is licensed under a GPLv3 licence with CSIRO Disclaimer


Installation

LOCALIZER has been written in Python and uses pepstats from the EMBOSS software and the WEKA 3.6 software. It also requires that you have Perl and BioPython installed.

To get LOCALIZER to work on your local machine, you need to install the EMBOSS and WEKA softwares from source. Both are already provided in the LOCALIZER distribution to ensure that compatible versions are used.

1. Unpack LOCALIZER in your desired location

  • tar xvf LOCALIZER_1.0.tar.gz
    cd LOCALIZER_1.0
  • 2. For the EMBOSS installation, you need to switch to the Scripts directory and unpack, configure and make

  • cd Scripts
    tar xvf emboss-latest.tar.gz
    cd EMBOSS-6.5.7/
    ./configure
    make
    cd ../
  • 3. For WEKA, you need to simply unzip the file weka-3-6-12.zip

  • unzip weka-3-6-12.zip
  • If you are having troube installing EMBOSS, please see here for help.
    If you are having troube installing WEKA, please see here for help.

    4. Test if LOCALIZER is working

  • python LOCALIZER.py -e -i Effector_Testing.fasta
  • 5. Problems?

    If you are getting an error message like 'ImportError: No module named Bio', you need to install BioPython on your computer. See here for help. For example, you can try and run 'pip install biopython'.

    Note also that you need PERL to be installed on your computer for running NLStradamus.

    Make sure that your input sequences in FASTA format have proper identifiers, if you only supply the empty identifier '>' LOCALIZER will fail.


    Contact

    For comments and suggestions regarding the code please contact jana.sperschneider@csiro.au