Bio::Tools::Run::Vista(3pm)				User Contributed Perl Documentation			       Bio::Tools::Run::Vista(3pm)

NAME

       Bio::Tools::Run::Vista

       Wrapper for Vista

SYNOPSIS

	 use Bio::Tools::Run::Vista;
	 use Bio::Tools::Run::Alignment::Lagan;
	 use Bio::AlignIO;

	 my $sio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'genbank');
	 my @seq;
	 my $reference = $sio->next_seq;
	 push @seq, $reference;
	 while(my $seq = $sio->next_seq){
	   push @seq,$seq;
	 }
	 my @features = grep{$_->primary_tag eq 'CDS'} $reference->get_SeqFeatures;

	 my $lagan = Bio::Tools::Run::Alignment::Lagan->new;

	 my $aln = $lagan->mlagan(@seq,'(fugu (mouse human))');

	 my $vis = Bio::Tools::Run::Vista->new('outfile'=>"outfile.pdf",
					       'title' => "My Vista Plot",
					       'annotation'=>@features,
					       'annotation_format'=>'GFF',
					       'min_perc_id'=>75,
					       'min_length'=>100,
					       'plotmin'   => 50,
					       'tickdist' => 2000,
					       'window'=>40,
					       'numwindows'=>4,
					       'start'=>50,
					       'end'=>1500,
					       'tickdist'=>100,
					       'bases'=>1000,
					       'java_param'=>"-Xmx128m",
					       'num_pages'=>1,
					       'color'=> {'EXON'=>'100 0 0',
							  'CNS'=>'0 0 100'},
					       'quiet'=>1);

	 my $referenceid= 'human';
	 $vis->run($aln,$referenceid);

	 #alternative one can choose pairwise alignments to plot
	 #where the second id in each pair is the reference sequence
	 $vis->run($aln,([mouse,human],[fugu,human],[mouse,fugu]));

DESCRIPTION

       Pls see Vista documentation for plotfile options

       Wrapper for Vista :

       C. Mayor, M. Brudno, J. R. Schwartz, A. Poliakov, E. M. Rubin, K. A.  Frazer, L. S. Pachter, I. Dubchak.  VISTA: Visualizing global DNA
       sequence alignments of arbitrary length.  Bioinformatics, 2000  Nov;16(11):1046-1047.  Get it here:
       http://www-gsd.lbl.gov/vista/VISTAdownload2.html

       On the command line, it is assumed that this can be executed:

       java Vista plotfile

       Some of the code was adapted from MLAGAN toolkit

       M. Brudno,  C.B. Do,  G. Cooper,  M.F. Kim,  E. Davydov,  NISC Sequencing Consortium, E.D. Green,  A. Sidow and S. Batzoglou LAGAN and
       Multi-LAGAN: Efficient Tools for Large-Scale Multiple  Alignment of Genomic DNA, Genome Research, in press

       get lagan here:

       http://lagan.stanford.edu/

FEEDBACK

   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

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

       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.

   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/

AUTHOR

       Shawn Hoon Email shawnh@fugu-sg.org

APPENDIX

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

   new
	   Title   :   new
	   Usage   :   my $vis = Bio::Tools::Run::Vista->new('outfile'=>$out,
					       'title' => "My Vista Plot",
					       'annotation'=>@features,
					       'annotation_format'=>'GFF',
					       'min_perc_id'=>75,
					       'min_length'=>100,
					       'plotmin'   => 50,
					       'tickdist' => 2000,
					       'window'=>40,
					       'numwindows'=>4,
					       'start'=>50,
					       'end'=>1500,
					       'tickdist'=>100,
					       'bases'=>1000,
					       'color'=> {'EXON'=>'100 0 0',
							  'CNS'=>'0 0 100'},
					       'quiet'=>1);
	   Function:   Construtor for Vista wrapper
	   Args    :   outfile - location of the pdf generated
		       annotation - either a file or and array ref of Bio::SeqFeatureI
				    indicating the exons
		       regmin	  -region min

   java
	   Title   :   java
	   Usage   :   $obj->java('/usr/opt/java130/bin/java');
	   Function:   Get/set method for the location of java VM
	   Args    :   File path (optional)

   run
	Title	: run
	Usage	: my @genes = $self->run($seq)
	Function: runs Vista
	Returns : A boolean 1 if no errors
	Args	: Argument 1: Bio::Align::Align required
		  Argument 2: a string or number, which is the sequence id of the
			      reference sequence or the rank of the sequence
			      in the alignment

   _setinput
	Title	: _setinput
	Usage	: Internal function, not to be called directly
	Function: writes input sequence to file and return the file name
	Example :
	Returns : string
	Args	:

   outfile
	 Title	  : outfile
	 Usage	  : $obj->outfile
	 Function : Get/Set method outfile
	 Args	  :

   min_perc_id
	 Title	  : min_perc_id
	 Usage	  : $obj->min_perc_id
	 Function : Get/Set method min_perc_id
	 Args	  :

   quiet
	 Title	  : quiet
	 Usage	  : $obj->quiet
	 Function : Get/Set method quiet
	 Args	  :

   verbose
	 Title	  : verbose
	 Usage	  : $obj->verbose
	 Function : Get/Set method verbose
	 Args	  :

   annotation_format
	 Title	  : annotation_format
	 Usage	  : $obj->annotation_format
	 Function : Get/Set method annotation_format
	 Args	  :

   region_file
	 Title	  : region_file
	 Usage	  : $obj->region_file
	 Function : Get/Set method region_file
	 Args	  :

   score_file
	 Title	  : score_file
	 Usage	  : $obj->score_file
	 Function : Get/Set method score_file
	 Args	  :

   alignment_file
	 Title	  : alignment_file
	 Usage	  : $obj->alignment_file
	 Function : Get/Set method alignment_file
	 Args	  :

   contigs_file
	 Title	  : contigs_file
	 Usage	  : $obj->contigs_file
	 Function : Get/Set method contigs_file
	 Args	  :

   diffs
	 Title	  : diffs
	 Usage	  : $obj->diffs
	 Function : Get/Set method diffs
	 Args	  :

   plotfile
	 Title	  : plotfile
	 Usage	  : $obj->plotfile
	 Function : Get/Set method plotfile
	 Args	  :

   min_length
	 Title	  : min_length
	 Usage	  : $obj->min_length
	 Function : Get/Set method min_length
	 Args	  :

   plotmin
	 Title	  : plotmin
	 Usage	  : $obj->plotmin
	 Function : Get/Set method plotmin
	 Args	  :

   annotation
	 Title	  : annotation
	 Usage	  : $obj->annotation
	 Function : Get/Set method annotation
	 Args	  :

   bases
	 Title	  : bases
	 Usage	  : $obj->bases
	 Function : Get/Set method bases
	 Args	  :

   tickdist
	 Title	  : tickdist
	 Usage	  : $obj->tickdist
	 Function : Get/Set method tickdist
	 Args	  :

   resolution
	 Title	  : resolution
	 Usage	  : $obj->resolution
	 Function : Get/Set method resolution
	 Args	  :

   title
	 Title	  : title
	 Usage	  : $obj->title
	 Function : Get/Set method title
	 Args	  :

   window
	 Title	  : window
	 Usage	  : $obj->window
	 Function : Get/Set method window
	 Args	  :

   numwindows
	 Title	  : numwindows
	 Usage	  : $obj->numwindows
	 Function : Get/Set method numwindows
	 Args	  :

   start
	 Title	  : start
	 Usage	  : $obj->start
	 Function : Get/Set method start
	 Args	  :

   end
	 Title	  : end
	 Usage	  : $obj->end
	 Function : Get/Set method end
	 Args	  :

   num_plot_lines
	 Title	  : num_plot_lines
	 Usage	  : $obj->num_plot_lines
	 Function : Get/Set method num_plot_lines
	 Args	  :

   legend
	 Title	  : legend
	 Usage	  : $obj->legend
	 Function : Get/Set method legend
	 Args	  :

   filename
	 Title	  : filename
	 Usage	  : $obj->filename
	 Function : Get/Set method filename
	 Args	  :

   axis_label
	 Title	  : axis_label
	 Usage	  : $obj->axis_label
	 Function : Get/Set method axis_label
	 Args	  :

   ticks_file
	 Title	  : ticks_file
	 Usage	  : $obj->ticks_file
	 Function : Get/Set method ticks_file
	 Args	  :

   color
	 Title	  : color
	 Usage	  : $obj->color
	 Function : Get/Set method color
	 Args	  :

   use_order
	 Title	  : use_order
	 Usage	  : $obj->use_order
	 Function : Get/Set method use_order
	 Args	  :

   gaps
	 Title	  : gaps
	 Usage	  : $obj->gaps
	 Function : Get/Set method gaps
	 Args	  :

   snps_file
	 Title	  : snps_file
	 Usage	  : $obj->snps_file
	 Function : Get/Set method snps_file
	 Args	  :

   repeats_file
	 Title	  : repeats_file
	 Usage	  : $obj->repeats_file
	 Function : Get/Set method repeats_file
	 Args	  :

   filter_repeats
	 Title	  : filter_repeats
	 Usage	  : $obj->filter_repeats
	 Function : Get/Set method filter_repeats
	 Args	  :

perl v5.12.3							    2011-06-18					       Bio::Tools::Run::Vista(3pm)