Bio::Tools::Run Vista
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Summary
Bio::Tools::Run::Vista
Wrapper for Vista
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Bio::Root::Root
Bio::Seq
Bio::Tools::Run::WrapperBase
File::Copy
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
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/
Methods
BEGIN Code
AUTOLOAD
No description
Code
newDescriptionCode
executable
No description
Code
javaDescriptionCode
runDescriptionCode
_setinputDescriptionCode
_parse_multi_fasta
No description
Code
_mf2bin
No description
Code
_pack_bin
No description
Code
_make_plotfile
No description
Code
_dump2gff
No description
Code
_run_Vista
No description
Code
_coordinate
No description
Code
Methods description
newcode    nextTop
    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
javacodeprevnextTop
    Title   :   java
    Usage   :   $obj->java('/usr/opt/java130/bin/java');
    Function:   Get/set method for the location of java VM
    Args    :   File path (optional)
runcodeprevnextTop
 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
_setinputcodeprevnextTop
 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    :
Methods code
BEGINTop
BEGIN {
    $PROGRAMNAME = 'java';

    if( ! defined $PROGRAMDIR ) {
    	$PROGRAMDIR = $ENV{'JAVA_HOME'} || $ENV{'JAVA_DIR'};
    }
    if (defined $PROGRAMDIR) {
    	foreach my $progname ( [qw(java)],[qw(bin java)] ) {
  	    my $f = Bio::Root::IO->catfile($PROGRAMDIR, @$progname);
  	    if( -e $f && -x $f ) {
      		$PROGRAM = $f;
      		last;
  	    }
    	}
    }

    %DEFAULT_VALUES= ('java'     => 'java',
                      'min_perc_id'   => 75,
                      'min_length'   => 100,
                      'plotmin'      => 50,
                      'bases'    => 10000,
                      'tickdist' => 2000,
                      'resolution'=> 25,
                      'window'  => 40,
                      'title'   => 'VISTA PLOT',
                      'numwindows'=>4);

    @VISTA_PARAMS=qw(JAVA JAVA_PARAM OUTFILE MIN_PERC_ID QUIET VERBOSE ANNOTATION_FORMAT
                     REGION_FILE REGION_FILE_DIR SCORE_FILE SCORE_FILE_DIR ALIGNMENT_FILE_DIR
                     ALIGNMENT_FILE CONTIGS_FILE DIFFS PLOTFILE
                     MIN_LENGTH PLOTMIN ANNOTATION BASES TICKDIST RESOLUTION TITLE PAPER
                     WINDOW NUMWINDOWS START END NUM_PLOT_LINES LEGEND FILENAME NUM_PAGES
                     AXIS_LABEL TICKS_FILE COLOR USE_ORDER GAPS SNPS_FILE REPEATS_FILE 
                     FILTER_REPEATS);

    foreach my $attr ( @VISTA_PARAMS)
    { $OK_FIELD{$attr}++;
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
    my $self = shift;
    my $attr = $AUTOLOAD;
    $self->debug( "************ attr:  $attr\n");
    $attr =~ s/.*:://;
    $attr = uc $attr;
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr} = shift if @_;
    return $self->{$attr};
}
newdescriptionprevnextTop
sub new {
    my ($caller, @args) = @_;
    # chained new
    my $self = $caller->SUPER::new(@args);
    # so that tempfiles are cleaned up
    foreach my $key(keys %DEFAULT_VALUES){
      $self->$key($DEFAULT_VALUES{$key});
    }
    while (@args)  {
       my $attr =   shift @args;
       my $value =  shift @args;
       next if( $attr =~ /^-/ ); # don't want named parameters
	    $self->$attr($value);
    }

    return $self;
}
executabledescriptionprevnextTop
sub executable {
 shift->java(@_);
}
javadescriptionprevnextTop
sub java {
   my ($self, $exe,$warn) = @_;

   if( defined $exe ) {
     $self->{'_pathtojava'} = $exe;
   }

   unless( defined $self->{'_pathtojava'} ) {
       if( $PROGRAM && -e $PROGRAM && -x $PROGRAM ) {
	   $self->{'_pathtojava'} = $PROGRAM;
       } else {
	   my $exe;
	   if( ( $exe = $self->io->exists_exe($PROGRAMNAME) ) &&
	       -x $exe ) {
	       $self->{'_pathtojava'} = $exe;
	   } else {
	       $self->warn("Cannot find executable for $PROGRAMNAME") if $warn;
	       $self->{'_pathtojava'} = undef;
	   }
       }
   }
   $self->{'_pathtojava'};
}
rundescriptionprevnextTop
sub run {
    my ($self,$align,$ref) = @_;
    $ref ||=1;
    my $infile = $self->_setinput($align,$ref);
    return $self->_run_Vista($infile);
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($self,$sim_aln,$ref) = @_;
    my($pairs,$files) = $self->_mf2bin($sim_aln,$ref);
    my $plotfile = $self->_make_plotfile($sim_aln,$pairs,$files);
    return $plotfile;
}
_parse_multi_fastadescriptionprevnextTop
sub _parse_multi_fasta {
  my ($self,$file) = @_;
  my %seq;
  open(FASTA, $file) || $self->throw("Couldn't open $file");
  my $last;
  my $count = 0;
  while (my $line = <FASTA>) {
    chomp $line;
    next if $line=~/^$/;
    if (substr($line, 0, 1) eq ">") {
        $_ = substr($line, 1);
        /\w+/g;
        $seq{$&} = "";
        $last = $&;
    } else {
        $seq{$last}.=$line;
    }
    print STDERR $count."\n";
    $count++;
  }
  my @seq;

  foreach my $key(keys %seq){
    my $seq = Bio::Seq->new(-id=>$key,-seq=>$seq{$key});
    push @seq,$seq;
  }
  return @seq;
}

#adapted from mlagan utils  mf2bin.pl
}
_mf2bindescriptionprevnextTop
sub _mf2bin {
  my ($self,$sim,$ref)= @_;
  my @seq;
  if(!ref $sim){
    @seq = $self->_parse_multi_fasta($sim);
  }
  else {
    ($sim && $sim->isa("Bio::Align::AlignI")) || $self->throw("Expecting a Bio::Align::AlignI");
    @seq = $sim->each_seq;
  }
  my $reference;
  my @files;
  my @pairs;
  if(ref($ref) eq 'ARRAY'){
    my @ref;
    foreach my $set(@$ref){
      my ($reference) = grep{$_->id eq $set->[1]}@seq;
      my ($other) = grep{$_->id eq $set->[0]}@seq;
      my ($pair,$file) = $self->_pack_bin($reference,$other);
      push @pairs, @$pair;
      push @files, @$file;
      push @ref,$set->[1];
    }
    $self->_coordinate(\@ref);
    return\@ pairs,\@files;

  }
  #figure out the reference sequence
  elsif($ref =~/^\d+$/){ #its a rank index
    $reference = $seq[$ref-1];
    my $tmp = $ref;
    $ref = $reference->id;
    splice @seq,($tmp-1),1;
  }
  else { #its an id
    foreach my $i(0..$#seq){
      if($seq[$i]->id =~/$ref/){
        $reference  = $seq[$i];
        splice @seq,($i),1;
        last;
      }
    }
  }
  $self->_coordinate([$ref]);

  # pack bin
  # format from Alex Poliakov's glass2bin.pl script
  my %base_code = ('-' => 0, 'A' => 1, 'C' => 2, 'T' => 3, 'G' => 4, 'N' => 5,
                'a' => 1, 'c' => 2, 't' => 3, 'g' => 4, 'n' => 5);


 my @ref= (split ('',$reference->seq));

  foreach my $seq2(@seq){
      my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir);
      my @seq2= (split('', $seq2->seq)); 
      foreach my $index(0..$#ref){
        unless($ref[$index] eq '-' && $seq2[$index] eq '-'){
          print $tfh1 pack("H2",$base_code{$ref[$index]}.$base_code{$seq2[$index]});
        }
      }
      close ($tfh1);
      undef ($tfh1);
      push @files, $outfile;
      push @pairs,[$reference->id,$seq2->id];
  }
  return\@ pairs,\@files;
}
_pack_bindescriptionprevnextTop
sub _pack_bin {
  my ($self,$first,$sec) = @_;
  my @first = (split('',$first->seq));
  my @sec = (split('',$sec->seq));
  # pack bin
  # format from Alex Poliakov's glass2bin.pl script
  my %base_code = ('-' => 0, 'A' => 1, 'C' => 2, 'T' => 3, 'G' => 4, 'N' => 5,
                'a' => 1, 'c' => 2, 't' => 3, 'g' => 4, 'n' => 5);
  my @files;
  my @pairs;
  my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir);
  foreach my $index(0..$#first){
    unless($first[$index] eq '-' && $sec[$index] eq '-'){
      print $tfh1 pack("H2",$base_code{$first[$index]}.$base_code{$sec[$index]});
    }
  }
  close ($tfh1);
  undef ($tfh1);
  push @files, $outfile;
  push @pairs,[$first->id,$sec->id];
  return\@ pairs,\@files;
}
_make_plotfiledescriptionprevnextTop
sub _make_plotfile {
  my ($self,$sim_aln,$pairs,$files) = @_;
  my ($tfh1,$plotfile) = $self->io->tempfile(-dir=>$self->tempdir);
  my @ids = map{$_->id}$sim_aln->each_seq;
  
  print $tfh1 "TITLE ".$self->title."\n\n";
  print $tfh1 "OUTPUT ".$self->outfile."\n\n" ;
  print $tfh1 "SEQUENCES ";
  print $tfh1 join(" ",@ids)."\n\n";

  foreach my $index(0..$#$pairs){
    print $tfh1 "ALIGN ".$files->[$index]." BINARY\n";
    print $tfh1 " SEQUENCES ".$pairs->[$index]->[0]." ".$pairs->[$index]->[1]."\n";
    print $tfh1 " REGIONS ".$self->min_perc_id." ".$self->min_length."\n";
    print $tfh1 " MIN ".$self->plotmin."\n";
    print $tfh1 " DIFFS ". $self->diffs ."\n\n" if $self->diffs;
    if($self->region_file||$self->region_file_dir){
      my $file = " REGION_FILE ";
      $file.=$self->region_file_dir."/" if $self->region_file_dir;
      $file.=$pairs->[$index]->[0]."_".$pairs->[$index]->[1].".region\n\n";
      print $tfh1 $file;
    }
    if($self->score_file || $self->score_file_dir){
      my $file = " SCORE_FILE ";
      $file.=$self->score_file_dir."/" if $self->score_file_dir;
      $file.=$pairs->[$index]->[0]."_".$pairs->[$index]->[1].".score\n\n";
      print $tfh1 $file;
    }
    if($self->alignment_file || $self->alignment_file_dir){
      my $file = " ALIGNMENT_FILE ";
      $file.=$self->alignment_file_dir."/" if $self->alignment_file_dir;
      $file.=$pairs->[$index]->[0]."_".$pairs->[$index]->[1].".alignment\n\n";
      print $tfh1 $file;
    }
       
    print $tfh1 " CONTIGS_FILE ". $self->contigs_file ."\n\n" if $self->contigs_file;
    print $tfh1 " USE_ORDER ". $self->use_order."\n\n" if $self->use_order;
    print $tfh1 "END\n\n ";
  }
  my $annotation_file;
  if((ref $self->annotation eq 'ARRAY')&& $self->annotation->[0]->isa("Bio::SeqFeatureI")){
    $annotation_file = $self->_dump2gff($self->annotation);
    $self->annotation_format('GFF');
  }
  elsif($self->annotation){
    $annotation_file = $self->annotation;
  }
  $annotation_file .= " GFF" if $self->annotation_format=~/GFF/i;
  print $tfh1 "GENES ".$annotation_file."\n\n " if $annotation_file;
  print $tfh1 "LEGEND on\n\n";
  print $tfh1 "COORDINATE ".join(" ",@{$self->_coordinate})."\n\n";
  print $tfh1 "PAPER letter\n\n";
  print $tfh1 "BASES ".$self->bases."\n\n";
  print $tfh1 "TICK_DIST ".$self->tickdist."\n\n";
  print $tfh1 "RESOLUTION ".$self->resolution."\n\n";
  print $tfh1 "WINDOW ".$self->window."\n\n";
  print $tfh1 "NUM_WINDOWS ".$self->numwindows."\n\n";
  print $tfh1 "AXIS_LABEL ".$self->axis_label ."\n\n" if $self->axis_label;
  print $tfh1 "TICKS_FILE ".$self->ticks_file ."\n\n" if $self->ticks_file;
  print $tfh1 "SNPS_FILE"." ".$self->snps_file."\n\n" if $self->snps_file;
  print $tfh1 "GAPS ".$self->gaps ."\n\n"if $self->gaps;
  print $tfh1 "REPEATS_FILE ".$self->repeats_file ."\n\n" if $self->repeats_file;
  print $tfh1 "FILTER_REPEATS ".$self->filter_repeats ."\n\n" if $self->filter_repeats;
  print $tfh1 "NUM_PAGES ".$self->num_pages ."\n\n" if $self->num_pages;
  print $tfh1 "START ".$self->start ."\n\n" if $self->start;
  print $tfh1 "END ".$self->end ."\n\n" if $self->end;
  my $color = $self->color;
  if(ref $color eq 'HASH'){
    foreach my $region_type (keys %$color){
      print $tfh1 "COLOR ".$region_type." ".$color->{$region_type}."\n\n";
    }
  }

  close ($tfh1);
  undef $tfh1;
  if($self->plotfile) {#saving plotfile
    copy($plotfile,$self->plotfile);
  } 
  else {
    $self->plotfile($plotfile);
  }
  return $self->plotfile;
}
_dump2gffdescriptionprevnextTop
sub _dump2gff {
  my ($self,$feat) = @_;
  my ($tfh1,$file) = $self->io->tempfile(-dir=>$self->tempdir);
  foreach my $f(@$feat){
    print $tfh1 $f->gff_string."\n";
  }
  close ($tfh1);
  undef $tfh1;
  return $file;
}
_run_VistadescriptionprevnextTop
sub _run_Vista {
    my ($self,$infile) = @_;

    #run Vista
    $self->debug( "Running Vista\n");
    my $java = $self->java;
    my $param = $self->java_param || '';
    my $cmd  =   $java." ".$param.' Vista ';
    $cmd .= " -q " if $self->quiet || $self->verbose < 0;
    $cmd .= " -d " if $self->debug;
    $cmd .= $infile;
    $self->debug($cmd);
	 my $status = system ($cmd);

   $self->throw("Problem running Vista: $?\n ") if $status != 0;
   
   return 1;
}
_coordinatedescriptionprevnextTop
sub _coordinate {
  my ($self,$val) = @_;
  if($val){
    $self->{'_coordinate'} = $val;
  }
  return $self->{'_coordinate'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHORTop
Shawn Hoon
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
outfileTop
  Title    : outfile
  Usage    : $obj->outfile
  Function : Get/Set method outfile
  Args     :
min_perc_idTop
  Title    : min_perc_id
  Usage    : $obj->min_perc_id
  Function : Get/Set method min_perc_id
  Args     :
quietTop
  Title    : quiet
  Usage    : $obj->quiet
  Function : Get/Set method quiet
  Args     :
verboseTop
  Title    : verbose
  Usage    : $obj->verbose
  Function : Get/Set method verbose
  Args     :
annotation_formatTop
  Title    : annotation_format
  Usage    : $obj->annotation_format
  Function : Get/Set method annotation_format
  Args     :
region_fileTop
  Title    : region_file
  Usage    : $obj->region_file
  Function : Get/Set method region_file
  Args     :
score_fileTop
  Title    : score_file
  Usage    : $obj->score_file
  Function : Get/Set method score_file
  Args     :
alignment_fileTop
  Title    : alignment_file
  Usage    : $obj->alignment_file
  Function : Get/Set method alignment_file
  Args     :
contigs_fileTop
  Title    : contigs_file
  Usage    : $obj->contigs_file
  Function : Get/Set method contigs_file
  Args     :
diffsTop
  Title    : diffs
  Usage    : $obj->diffs
  Function : Get/Set method diffs
  Args     :
plotfileTop
  Title    : plotfile
  Usage    : $obj->plotfile
  Function : Get/Set method plotfile
  Args     :
min_lengthTop
  Title    : min_length
  Usage    : $obj->min_length
  Function : Get/Set method min_length
  Args     :
plotminTop
  Title    : plotmin
  Usage    : $obj->plotmin
  Function : Get/Set method plotmin
  Args     :
annotationTop
  Title    : annotation
  Usage    : $obj->annotation
  Function : Get/Set method annotation
  Args     :
basesTop
  Title    : bases
  Usage    : $obj->bases
  Function : Get/Set method bases
  Args     :
tickdistTop
  Title    : tickdist
  Usage    : $obj->tickdist
  Function : Get/Set method tickdist
  Args     :
resolutionTop
  Title    : resolution
  Usage    : $obj->resolution
  Function : Get/Set method resolution
  Args     :
titleTop
  Title    : title
  Usage    : $obj->title
  Function : Get/Set method title
  Args     :
windowTop
  Title    : window
  Usage    : $obj->window
  Function : Get/Set method window
  Args     :
numwindowsTop
  Title    : numwindows
  Usage    : $obj->numwindows
  Function : Get/Set method numwindows
  Args     :
startTop
  Title    : start
  Usage    : $obj->start
  Function : Get/Set method start
  Args     :
endTop
  Title    : end
  Usage    : $obj->end
  Function : Get/Set method end
  Args     :
num_plot_linesTop
  Title    : num_plot_lines
  Usage    : $obj->num_plot_lines
  Function : Get/Set method num_plot_lines
  Args     :
legendTop
  Title    : legend
  Usage    : $obj->legend
  Function : Get/Set method legend
  Args     :
filenameTop
  Title    : filename
  Usage    : $obj->filename
  Function : Get/Set method filename
  Args     :
axis_labelTop
  Title    : axis_label
  Usage    : $obj->axis_label
  Function : Get/Set method axis_label
  Args     :
ticks_fileTop
  Title    : ticks_file
  Usage    : $obj->ticks_file
  Function : Get/Set method ticks_file
  Args     :
colorTop
  Title    : color
  Usage    : $obj->color
  Function : Get/Set method color
  Args     :
use_orderTop
  Title    : use_order
  Usage    : $obj->use_order
  Function : Get/Set method use_order
  Args     :
gapsTop
  Title    : gaps
  Usage    : $obj->gaps
  Function : Get/Set method gaps
  Args     :
snps_fileTop
  Title    : snps_file
  Usage    : $obj->snps_file
  Function : Get/Set method snps_file
  Args     :
repeats_fileTop
  Title    : repeats_file
  Usage    : $obj->repeats_file
  Function : Get/Set method repeats_file
  Args     :
filter_repeatsTop
  Title    : filter_repeats
  Usage    : $obj->filter_repeats
  Function : Get/Set method filter_repeats
  Args     :