view release on metacpan or  search on metacpan

lib/Bio/Tools/Run/Alignment/Kalign.pm  view on Meta::CPAN

#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Albert Vilella
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Alignment::Kalign - Object for the calculation of an
iterative multiple sequence alignment from a set of unaligned
sequences or alignments using the KALIGN program

=head1 SYNOPSIS

  # Build a kalign alignment factory
  $factory = Bio::Tools::Run::Alignment::Kalign->new(@params);

  # Pass the factory a list of sequences to be aligned.
  $inputfilename = 't/cysprot.fa';
  # $aln is a SimpleAlign object.
  $aln = $factory->align($inputfilename);

  # or where @seq_array is an array of Bio::Seq objects
  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);

  # Or one can pass the factory a pair of (sub)alignments
  #to be aligned against each other, e.g.:

  #There are various additional options and input formats available.
  #See the DESCRIPTION section that follows for additional details.

=head1 DESCRIPTION

Please cite:

        Timo Lassmann and Erik L.L. Sonnhammer (2005)
        Kalign - an accurate and fast multiple sequence alignment algorithm.
        BMC Bioinformatics 6:298

http://msa.cgb.ki.se/downloads/kalign/current.tar.gz


=head2 Helping the module find your executable 

You will need to enable Kalign to find the kalign program. This can be
done in (at least) three ways:

  1. Make sure the kalign executable is in your path (i.e. 
     'which kalign' returns a valid program
  2. define an environmental variable KALIGNDIR which points to a 
     directory containing the 'kalign' app:
   In bash 
	export KALIGNDIR=/home/progs/kalign   or
   In csh/tcsh
        setenv KALIGNDIR /home/progs/kalign

  3. include a definition of an environmental variable KALIGNDIR 
      in every script that will
     BEGIN {$ENV{KALIGNDIR} = '/home/progs/kalign'; }
     use Bio::Tools::Run::Alignment::Kalign;

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the web:

 http://redmine.open-bio.org/projects/bioperl/

=head1 AUTHOR -  Albert Vilella

Email idontlikespam@hotmail.com

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut

package Bio::Tools::Run::Alignment::Kalign;

use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM %DEFAULTS
            @KALIGN_PARAMS @KALIGN_SWITCHES %OK_FIELD
            );
use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use  Bio::Tools::Run::WrapperBase;