Bio::Tools::Run::Vista.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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://bugzilla.open-bio.org/
 
 

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     :