Felipe da Veiga Leprevost
and 1 contributors

Name

Bio::Tools::Alignment::Overview - just another represetation for biological sequence alignment.

Description

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.

Basic Usage

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();

Methods

For the moment the only customization available is the color for the sequences.

Input
        $object->input();

The module is compatible with alignments generated by other programs like ClustalW, MUSCLE and T-COFEE.

Output
        $object->output();

No extension is required for the output file, the module generates automatically a .png file.

Color
        $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.

Make_image
        $object->make_image();

This is the method responsible for generating the image file with png extension.

Author

Leprevost, <leprevostfv at gmail.com>

How to cite this work

Please refer to the following DOI in order to cite this module.

DOI

Bugs

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.

Support

You can find documentation for this module with the perldoc command.

    perldoc Bio::Tools::Alignment::Overview

You can also look for information at:

License and Copyright

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.

See Also

GD::Simple