Bio::Tools::Protscale

Protscale.pm

package Bio::Tools::Protscale;
use strict;
use warnings;
use base qw(Bio::Root::Root);
use LWP 5.64;
use HTML::TreeBuilder::XPath;
use Data::Dumper;

=head1 NAME

  Bio::Tools::Protscale

=head1 SYNOPSYS

  my $chart = Bio::Tools::Protscale->new(seq => $seq);
  $chart->result('gif');
  $chart->result_to_file('gif', 'path/to/file.gif');

=head1 METHOD

=head2 new(seq => Bio::SeqI)

=head2 result(FORMAT)

=head3 result_to_file(FORMAT, PATH)

=head1 AUTHOR
  
  hryk

=head1 SEE ALSO

=cut


sub new {
  my ($class, @args) = @_;
  @args = (
    '-base'      => 'http://www.expasy.org',
    '-url'       => '/cgi-bin/protscale.pl?1',
    '-form'      => 'sequence',
    '-scale'     => 'Hphob. / Kyte & Doolittle',
    '-window'    => 3,
    '-weight_variation' => 'linear',
    '-normalize' => 0,
    @args
  );

  my $self = $class->SUPER::new(@args);

  my ($base, $url, $seq, $form,
    $scale, $window, $weight_variation,
    $normalize ) = $self->_rearrange([
    qw/BASE URL SEQ FORM SCALE WINDOW WEIGHT_VARIATION NORMALIZE/],
    @args);

  $self->throw("Invalid argument : window size must be an odd number between 3 and 21") if ($window % 2 == 0) or ($window < 3);
  $self->throw("Invalid argument : 'normalize' should be 0 or 1.") unless $normalize == 0 or $normalize == 1;

  bless $self, $class;

  $self->_ua(LWP::UserAgent->new());
  $self->_base_uri($base);

  my $res;
  $res = $self->_ua->post($self->_base_uri.$url,
    [
      $form      => $seq,
      window     => $window,
      scale      => $scale,
      weight_var => $weight_variation,
      norm       => $normalize
    ],
    'User-Agent' => 'Mozilla/4.76 [en] (Win2000; U)',
  );

  $self->throw("$url error: ".$res->status_line) unless $res->is_success;
  $self->throw("Bad content type at $url ".$res->content_type) unless $res->content_type eq 'text/html';
  my $tree = HTML::TreeBuilder::XPath->new;
  $tree->parse($res->content);
  $self->_tree($tree);
  return $self;
}

sub chart {
  my $self = shift;
  my $nodes = $self->_tree->findnodes('//img[@alt="ProtScale graph"]');

  if ($nodes->size > 0) {
    my $src = $nodes->[0]->attr('src');
    my $res = $self->_ua->get($self->_base_uri.$src);
    if ($res->is_success) {
      $self->_image($res->content);
      return $self->_image;
    }
    else {
      $self->throw($res->status_line);
    }
  }
  else {
    $self->throw('Couldnot find chart image tag.');
  }
}

sub chart_to_file {
  my $self = shift;
  my $filename = shift;
  $self->chart();
  unless (defined $filename) {
    $self->throw('Empty filename.');
  }
  open my $fh,  ">$filename" || $self->throw("Cannt open file $filename: $!");
  $fh->print($self->_image);
  $fh->close;
}

sub _image {
  my $self = shift;
  if (scalar(@_) > 0) {
    $self->{_image} = shift;
  }
  return $self->{_image};
}

sub _ua {
  my $self = shift;
  if (scalar(@_) > 0) {
    $self->{_ua} = shift;
  }
  return $self->{_ua};
}

sub _tree {
  my $self = shift;
  if (scalar(@_) > 0) {
    $self->{_tree} = shift;
  }
  return $self->{_tree};
}

sub _base_uri {
  my $self = shift;
  if (scalar(@_) > 0) {
    $self->{_base_uri} = shift;
  }
  return $self->{_base_uri};
}

1;
__END__