Bio::Tools::Alignment::Overview - just another represetation for biological sequence alignment.
This module creates a simple and resumed representation of a biological sequence alignment. For now you can ajust the sequence color, with time new customizations will be implemented. If you find any problem please let me know.
instantiate the overview object.
use warnings; use strict; use Bio::Tools::Alignment::Overview(); my $view = Bio::Tools::Alignment::Overview->new();
and pass the required parameters.
$view->input('path_to_my_align_file'); $view->outup('path_to_my_output_file'); # no extension is required. $view->color('color_name'); # 'red'
create the image.
$view->make_image();
For the moment the only customization available is the color for the sequences.
$object->input();
The module is compatible with alignments generated by other programs like ClustalW, MUSCLE and T-COFEE.
$object->output();
No extension is required for the output file, the module generates automatically a .png file.
$object->color();
The module depends on GD::Simple for making the images files so the available colors are listed in GD::Simple. The default color is blue.
$object->make_image();
This is the method responsible for generating the image file with png extension.
Leprevost, <leprevostfv at gmail.com>
<leprevostfv at gmail.com>
Please report any bugs or feature requests to bug-bio-tools-alignment-overview at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Tools-Alignment-Overview. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
bug-bio-tools-alignment-overview at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Bio::Tools::Alignment::Overview
You can also look for information at:
RT: CPAN's request tracker (report bugs here)
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Tools-Alignment-Overview
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Bio-Tools-Alignment-Overview
CPAN Ratings
http://cpanratings.perl.org/d/Bio-Tools-Alignment-Overview
Search CPAN
http://search.cpan.org/dist/Bio-Tools-Alignment-Overview/
Copyright 2012 Leprevost.
This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.
See http://dev.perl.org/licenses/ for more information.
GD::Simple
To install Bio::Tools::Alignment::Overview, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Tools::Alignment::Overview
CPAN shell
perl -MCPAN -e shell install Bio::Tools::Alignment::Overview
For more information on module installation, please visit the detailed CPAN module installation guide.