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SANDPUMA

Specificity of AdenylatioN Domain Prediction Using Multiple Algorithms

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Copyright © 2016 Marc Chevrette

If you find SANDPUMA useful in your research, please cite: Chevrette et al., 2017 https://doi.org/10.1093/bioinformatics/btx400

This project is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This project is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program (filename LICENSE). If not, see http://www.gnu.org/licenses/.

This is the production repository of SANDPUMA and prediCAT.

The development repository can be found at bitbucket.org/chevrm/nrps2

Code/method contributors:

  • Marc Chevrette (chevrm at gmail dot com): Lead developer
  • Fabian Aicheler: SVM development
  • Marnix Medema: Developer/coordinator

Other key contributors:

  • Cameron Currie
  • Oliver Kohlbacher

Prerequisite software and packages:

  • python (packages: json, glob, re, sys, os, csv, scipy, sklearn, numpy)
  • perl (packages: Bio::SeqIO, Bio::TreeIO, Cwd 'abs_path')
  • mafft
  • FastTree
  • ClustalW
  • hmmscan (HMMER3)

INSTALLATION:

    ## ensure all above dependencies are installed

    ## Install dependencies listed in the apt repositories
    > sudo apt-get install python perl mafft ncbi-blast+ clustalw hmmer

    ## Install python dependencies with pip. If pip not installed,
    ## google how to set up pip
    > sudo pip install json glob re sys os csv scipy sklearn numpy

    ## Install bioperl through the CPAN shell
    > sudo perl -MCPAN -e shell
    ## Within the shell, enter below and choose defaults for all
    ## questions
       >> install Bio::SeqIO

    ## Download the FastTree executable and add to your path
    > wget http://www.microbesonline.org/fasttree/FastTree
    > sudo chmod 777 FastTree
    > nano ~/.bashrc
    ## Add FastTree to path
    ## e.g.:
        export PATH=$PATH:/path/to/FastTree
    > source ~/.bashrc

    ## set the SVM path

    ## List the current path
    > pwd -P
    ## Edit the SVM path
    > nano dependencies/NRPSPredictor2/NRPSpredictor2.sh
    ## Change the path in variable NRPSBASEDIR to the
    ## full path from pwd -P plus /dependencies/NRPSPredictor2
    ## e.g.:
        export NRPS2BASEDIR=/home/mchevrette/git/sandpuma/dependencies/NRPSPredictor2

Example Usages:

Update from a MIBiG json repository:

./update_nrps3.sh <MIBiG_json_dir>

Extract NRPS A-Domains from a nucleotide fasta:

./extract_adomains.sh <nucl.fna>

Run predictor on NRPS A-domains (protein):

./predictnrps.sh <adomains.faa> <SANDPUMA base dir>