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 listsSupport
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 minjava
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 :