Provided by: libbio-perl-run-perl_1.6.9-1_all bug

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     :