Perl modules for Polymorphic Loci Analysis (Polloc)

A collection of perl modules to analyse Polymorphic Loci in bacterial genomes.

Author

Luis M. Rodriguez R.

Institut de Recherche pour le developpement

UMR Resistance des Plantes aux Bioagresseurs

Group Effecteur/Cible

Montpellier, France

License

This package is licensed under the terms of The Artistic License. See LICENSE.txt.

Description

A perl package for detecting, comparing, grouping, extending and summarizing polymorphic loci in bacterial genomes. This package is mainly aimed to assist typing studies, but can be applied in a much wider range of projects.

Requirements

System-wide requirements

The basic system requires, at least, the following perl modules:

• Error

• File::Path

• File::Spec

• File::Temp

• List::Util

• Symbol

• Bio::SeqIO

Other requirements

The following requirements can be ignored depending on the set of modules to be used.

#### Perl modules:

• File::Basename

• Cwd

• Bio::Tools::Run::Alignment::Muscle

• Bio::Tools::Run::StandAloneBlast

• Bio::Tools::Run::Hmmer

• GD::Simple

External tools

• CRISPRfinder, for CRISPRs detection.

• TRF, for Tandem Repeats detection (producing Bio::Polloc::Locus::Repeat objects).

• mreps, for Repeats detection (alternative to TRF).

• Stand-Alone NCBI BLAST, for several analyses including features grouping, homology-based detection of features and context-based groups extension.

• Muscle, for alignments in features detection and grouping, as well as context-based groups extension.

• HMMER, for profiles-based features detection and as alternative to BLAST in context-based groups extension.

Installation

1. Install the requirements. Remember, you can find the Perl modules in CPAN.

2. Download the library. There are several alternatives, but we love git:

       mkdir Polloc
       cd Polloc
       git init
       git clone git://github.com/lmrodriguezr/Polloc
   

3. Install the library:

       # The following three lines are optional (only for non-built copies)
       perl Build.PL
       ./Build manifest
       ./Build dist
       
       # The following lines install the library and the documentation
       perl Makefile.PL
       make
       make test
       make install # Could require sudo
   

4. Use the package. See the following section (Usage) for some examples.

5. Familiar enough? We are glad to listen than, then you could start developing. You can check the documentation within the modules using perldoc (or any other Pod interpreter), or contact us for questions and feature requests.

Usage

### Running existing scripts

The scripts distributed with Polloc are located at the scripts folder. Scripts include a small help message, so that you can just run it with perl.

• Running the vntrs.pl script. This script is the core of the VNTRs analysis tool. It requires the vntrs.bme file, also at the scripts folder. Run it with no arguments to check the required parameters.

Writing new scripts

ToDo

F.A.Q.

How do I know the installed version of Polloc in my machine?

perl -MBio::Polloc -e 'print $Bio::Polloc::VERSION, "\n"'

Is there an implementation of Polloc running in a real-life tool?

Yes, the VNTRs detection tool, a web-service devoted to the detection and analysis of VNTR loci (Variable Number of Tandem Repeats). If you have another tool making use of Polloc, please let us know.

How can I contribute to the Polloc project?

The Polloc library is Open Source, and is licensed under the Perl Artistic License. This means that you can freely modify the code provided you properly cite the source. However, if you want your modifications to be incorporated into the main Polloc code, please fork Polloc at GitHub and submit your changes via Pull Requests. If you are not familiar with Git, please read the documentation available at the git website.