Bio-EnsEMBL
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lib/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm  view on Meta::CPAN 

  my $fh = $self->get_filehandle('gene_detailed_mapping_stats.txt', 'stats');

  my $fmt1 = "%-60s%-16s%-16s%-16s\n";
  my $fmt2 = "%-60s%5.0f (%7s) %5.0f (%7s) %5.0f (%7s)\n";
  my $fmt3 = "%3.2f%%";

  print $fh "Gene detailed mapping results:\n\n";

  print $fh sprintf($fmt1, "Gene type", "mapped", "lost (similar)",
    "lost (definite)");

  print $fh ('-'x108), "\n";

  foreach my $class (@{ $self->get_all_classes('source') }) {
    next if ($class eq 'all');

    my $total = $self->get_count_by_class('source', $class);

    # avoid division by zero error
    unless ($total) {
      $self->logger->warning("No count found for $class.\n", 1);
      next;
    }
    
    my $mapped = $self->get_count_by_subclass('source', $class, 'mapped');
    my $similar = $self->get_count_by_subclass('source', $class,
      'lost_similar');
    my $lost = $self->get_count_by_subclass('source', $class, 'lost_definite');

    print $fh sprintf($fmt2,
                      $class,
                      $mapped,  sprintf($fmt3, $mapped/$total*100),
                      $similar, sprintf($fmt3, $similar/$total*100),
                      $lost,    sprintf($fmt3, $lost/$total*100));
  }

  close($fh);
}


=head2 create_clicklist

  Example     : $analyser->create_clicklist;
  Description : Writes an html file which contains a list of all lost genes,
                with hyperlinks to the appropriate archive website. This is to
                manually check lost genes.
  Return type : none
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

=cut

sub create_clicklist {
  my $self = shift;

  my $fh = $self->get_filehandle('genes_lost.html', 'stats');

  # start html output
  print $fh qq(<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\n);
  print $fh qq(<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en-gb"  lang="en-gb">);
  print $fh "<head>\n";
  print $fh "<title>Lost genes ";
  print $fh $self->conf->param('sourcedbname'), ' -&gt; ',
            $self->conf->param('targetdbname');
  print $fh "</title>\n";
  print $fh "</head>\n<body>\n";

  my $prefix = $self->conf->param('urlprefix');
  unless ($prefix) {
    $self->logger->warning("No urlprefix set, clicklists might not be useable.\n", 1);
  }

  my $navigation;
  my $clicklist;

  foreach my $class (@{ $self->get_all_classes('source') }) {
    next if ($class eq 'all');

    $navigation .= "$class ";
    $clicklist .= "<h1>$class</h1>\n";
    
    foreach my $subclass (qw(lost_similar lost_definite)) {

      # navigation
      $navigation .= qq(<a href="#${class}-$subclass">$subclass</a> );
      
      # clicklist
      $clicklist .= "<h2>$subclass</h2>\n";

      foreach my $stable_id (@{ $self->get_all_by_subclass('source', $class, $subclass) }) {
        $clicklist .= qq(<a href="${prefix}$stable_id">$stable_id</a><br />\n);
      }
      
    }

    $navigation .= "<br />\n";
  }

  # print navigation and clicklist
  print $fh "$navigation\n\n";
  print $fh "$clicklist\n\n";

  # html footer
  print $fh "</body></html>\n";

  close($fh);
}


=head2 create_mapping_summary

  Example     : $analyser->create_mapping_summary();
  Description : Writes a text file containing a summary of the mapping stats.
                This will be emailed to the genebuilder for evaluation (you will
                have to manually send the email, using the text in
                "mapping_summary.txt" as the template).
  Return type : none
  Exceptions  : none
  Caller      : general



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