Bio::T...:Vista(3pm)

📦
version 1.7.3 · 3 versions
, in debian bookworm, ubuntu noble

💖 NAME 💖

Bio::Tools::Run::Vista — a wrapper for Vista, bestie. That's it, that's the module. (You're reading the Bio::Tools::Run::Vista man page, straight outta the User Contributed Perl Documentation corner of the internet. 🫶)

✨ 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 🌸

Okay so for the plotfile options, pls go see the Vista documentation — that's where the actual deets live, I'm just the messenger. 💅

This thing is a 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 the 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, no cap — the glow-up literally depends on you. 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. (Fr fr, the more context you give, the faster somebody can swoop in and save you. 🌈)

🐛 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 _ (iykyk — if you see that underscore, it's giving "private, don't touch").

⭐ 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 (yes, that typo is canon, we keep it 💀)
  • 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:

And that's the whole page, bestie — every single method, every single arg, nothing skipped, we ate and left no crumbs. 💅✨ This was perl v5.36.0 doing its thing back on 2023-01-22, and yeah, the page title up top really does read Bio::T...:Vista(3pm) because the docs truncate it like that. Stay iconic, go plot some genomes. 🦋🌸👑

📦 where this page comes from