DNA sequence callback

[Miquel Ramia]

Hi,

I'm trying to show the reference nucleotide sequence for some features
in a balloon popup. I've tryed with a callback using:

$self = shift;
$refseq = $self->dna;

but it's not working, how can I do it ?

thank you very much

Miquel Ramia

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[Dave Clements, GMOD Help Desk-2]

Hi Miquel,

If my Perl were better I might be able to tell you.  I'm attaching two
routines from the dna glyph that I'm hoping will make it easy for you
(or people with better Perl than mine) to figure out how to display
the sequence.  The dna glyph shows bases at high magnifications, and
%gc at lower magnifications.

Dave C


sub draw_component {
  my $self = shift;
  my $gd = shift;
  my ($x1,$y1,$x2,$y2) = $self->bounds(@_);

  my $dna        = eval { $self->feature->seq };
  $dna           = $dna->seq if ref($dna) and $dna->can('seq'); # to
catch Bio::PrimarySeqI objects
  $dna or return;

  # workaround for my misreading of interface -- LS
  $dna = $dna->seq if ref($dna) && $dna->can('seq');

  if ($self->dna_fits) {
    $self->draw_dna($gd,$dna,$x1,$y1,$x2,$y2);
  } elsif ($self->do_gc) {
    $self->draw_gc_content($gd,$dna,$x1,$y1,$x2,$y2);
  }
}

sub draw_dna {
  my $self = shift;

  my ($gd,$dna,$x1,$y1,$x2,$y2) = @_;
  my $pixels_per_base = $self->scale;
  my $feature = $self->feature;

  my $strand = $feature->strand || 1;
  $strand *= -1 if $self->{flip};

  my @bases = split '',$strand >= 0 ? $dna : $self->reversec($dna);

  my $color = $self->fgcolor;
  my $font  = $self->font;
  my $lineheight = $font->height;
  $y1 -= $lineheight/2 - 3;
  my $strands = $self->option('strand') || 'auto';

  my ($forward,$reverse);
  if ($strands eq 'auto') {
    $forward = $feature->strand >= 0;
    $reverse = $feature->strand <= 0;
  } elsif ($strands eq 'both') {
    $forward = $reverse = 1;
  } elsif ($strands eq 'reverse') {
    $reverse = 1;
  } else {
    $forward = 1;
  }
  # minus strand features align right, not left
  $x1 += $pixels_per_base - $font->width - 1 if $strand < 0;
  for (my $i=0;$i<@bases;$i++) {
    my $x = $x1 + $i * $pixels_per_base;
    $gd->char($font,$x+2,$y1,$bases[$i],$color)
           if $forward;
    $gd->char($font,$x+2,$y1+($forward ? $lineheight:0),
              $complement{$bases[$i]}||$bases[$i],$color)
    if $reverse;
  }

}

2009/11/10 Miquel Ràmia <miquel.ramia@...>:

> Hi,
>
> I'm trying to show the reference nucleotide sequence for some features
> in a balloon popup. I've tryed with a callback using:
>
> $self = shift;
> $refseq = $self->dna;
>
> but it's not working, how can I do it ?
>
> thank you very much
>
> Miquel Ramia
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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[Scott Cain-4]

Hi Miquel,

IIRC, the trick is that the dna method returns a Bio::Seq object, not
a dna string. To get the dna string, you have to call the seq method
on it, so like this:

  my $refseq = $self->dna->seq;

Scott

2009/11/10 Miquel Ràmia <miquel.ramia@...>:

> Hi,
>
> I'm trying to show the reference nucleotide sequence for some features
> in a balloon popup. I've tryed with a callback using:
>
> $self = shift;
> $refseq = $self->dna;
>
> but it's not working, how can I do it ?
>
> thank you very much
>
> Miquel Ramia
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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