Christopher Fields > BioPerl-Run > Bio::Tools::Run::Vista

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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     : 
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