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Polloc-1.5.3b
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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:

Other requirements

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

Perl modules:

External tools

Installation

From v1.5 onwards there are two way to install Polloc. The easiest way is using CPAN, with the command install Bio::Polloc.

The second way is from the source, in a three-steps process:

  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

Once installed, you can:

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.

ToDo: Documentation for:

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.

Where can I find the documented modules in human-readable format?

You can read the documentation of Polloc in HTML format at CPAN: (http://search.cpan.org/dist/Polloc/).

The tests failed, should I force installation?

It is very hard to predict the behavior your are going to experience with Polloc if you install it with failed tests. Instead, we prepared a generic troubleshooting for failed tests we have observed either at the CPAN tester matrix or running installations in our machines:

Test t/05-typing/02-typing.t failure 1

Are you reading a message like this?:

t/05-typing/02-typing.t ............ 1/13 Use of uninitialized value in concatenation (.) or string at /Library/Perl/5.10.0/Bio/Tools/Run/Alignment/Muscle.pm line 427.
sh: - : invalid option
Usage:	sh [GNU long option] [option] ...
	sh [GNU long option] [option] script-file ...
GNU long options:
	--debug
	--debugger
	--dump-po-strings
	--dump-strings
	--help
	--init-file
	--login
	--noediting
	--noprofile
	--norc
	--posix
	--protected
	--rcfile
	--restricted
	--verbose
	--version
	--wordexp
Shell options:
	-irsD or -c command or -O shopt_option		(invocation only)
	-abefhkmnptuvxBCHP or -o option

--------------------- WARNING ---------------------
MSG: Muscle call crashed: 512 [command  -in /tmp/_YS2FojZj7  -out /tmp/7BP7tE2dKG/fwsAmEh1NG 2> /dev/null]

---------------------------------------------------
Can't call method "average_percentage_identity" on an undefined value at /Users/luismrodriguezr/.cpan/build/Bio::Polloc-1.0503-xA5_RC/blib/lib/Bio/Polloc/LociGroup.pm line 376.
# Looks like you planned 13 tests but ran 6.
# Looks like your test exited with 2 just after 6.
t/05-typing/02-typing.t ............ Dubious, test returned 2 (wstat 512, 0x200)
Failed 7/13 subtests

This very verbose message often means one thing: you have Bio::Tools::Run::Alignment::Muscle installed in your system, but you don't have Muscle. The solution is pretty easy: install muscle, available at Robert Edgar's website.

Test t/05-typing/02-typing.t failure 2

Or, instead, are you reading a message like this?:

t/05-typing/02-typing.t ............ 1/13 sh: primersearch: command not found
t/05-typing/02-typing.t ............ 7/13 
#   Failed test 'The thing isa ARRAY'
#   at t/05-typing/02-typing.t line 35.
#     The thing isn't defined

#   Failed test at t/05-typing/02-typing.t line 36.
#          got: '-1'
#     expected: '0'

#   Failed test at t/05-typing/02-typing.t line 37.
#          got: undef
#     expected: '105'

#   Failed test at t/05-typing/02-typing.t line 42.
#          got: undef
#     expected: '1'
# Looks like you failed 4 tests of 13.
t/05-typing/02-typing.t ............ Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/13 subtests

This is far less verbose, but again means you lack required software in your machine. This time, it is the primersearch utility of EMBOSS. The solution: install EMBOSS, available at Sourceforge.

Other errors?

If you have non-listed failures, please do not hesitate to contact us, or directly register them at GitHub.