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

  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
  Status      : At Risk
              : under development

=cut

sub create_mapping_summary {
  my $self = shift;
  
  my $fh = $self->get_filehandle('mapping_summary.txt');

  #
  # title
  # 
  print $fh qq(Stable ID mapping results\n);
  print $fh qq(=========================\n\n);

  #
  # timing
  #
  print $fh "Run at:  ".localtime()."\n";
  print $fh "Runtime: ";
  print $fh $self->logger->runtime, "\n\n";

  #
  # parameters used for this run
  #
  print $fh $self->conf->list_param_values;
  print $fh "\n";

  #
  # mapping stats
  #
  foreach my $type (qw(exon transcript translation gene gene_detailed)) {
    my $filename = "${type}_mapping_stats.txt";
    
    if ($self->file_exists($filename, 'stats')) {
      print $fh $self->read_from_file($filename, 'stats');
      print $fh "\n\n";
    } else {
      print $fh "No mapping stats found for $type.\n\n";
    }
  }

  #
  # db uploads
  #
  my @uploads = (
    ['stable_ids'  => 'Stable IDs'],
    ['events'      => 'Stable ID events and mapping session'],
    ['archive'     => 'Gene and peptide archive'],
  );
  
  my $fmt1 = "%-40s%-20s\n";

  print $fh qq(Data uploaded to db:\n);
  print $fh qq(====================\n\n);

  if ($self->conf->param('dry_run')) {
   
    print $fh "None (dry run).\n";
  
  } else {
  
    foreach my $u (@uploads) {
      my $uploaded = 'no';
      $uploaded = 'yes' if ($self->conf->is_true("upload_".$u->[0]));
      print $fh sprintf($fmt1, $u->[1], $uploaded);
    }
    
  }

  print $fh "\n";

  #
  # stats and clicklist
  #
  my @output = (
    ['stats'    => 'statistics (including clicklists of deleted IDs)'],
    ['debug'    => 'detailed mapping output for debugging'],
    ['tables'   => 'data files for db upload'],
  );
  
  my $fmt2 = "%-20s%-50s\n";

  print $fh qq(\nOutput directories:\n);
  print $fh qq(===================\n\n);

  print $fh sprintf($fmt2, qw(DIRECTORY DESCRIPTION));
  print $fh ('-'x72), "\n";

  print $fh sprintf($fmt2, 'basedir', $self->conf->param('basedir'));

  foreach my $o (@output) {
    print $fh sprintf($fmt2, '$basedir/'.$o->[0], $o->[1]);
  }

  print $fh "\n";

  #
  # clicklist of first 10 deleted genes
  #
  print $fh qq(\nFirst 10 deleted known genes:\n);
  print $fh qq(=============================\n\n);

  my $in_fh = $self->get_filehandle('genes_lost.txt', 'debug', '<');
  my $prefix = $self->conf->param('urlprefix');
  my $i;
  
  while (<$in_fh>) {
    last if (++$i > 10);
    
    chomp;
    my ($stable_id, $type) = split(/\s+/);
    
    next unless ($type eq 'known');

    print $fh sprintf($fmt2, $stable_id, "${prefix}$stable_id");
  }

  close($in_fh);
  close($fh);
}


=head2 read_from_file

  Arg[1]      : String $filename - name of file to read
  Arg[2]      : (optional) String $append - directory name to append to basedir
  Example     : my $stats_text = $analyser->read_from_file('gene_mapping_stats',
                  'stats');
  Description : Reads mapping stats from a file.
  Return type : String
  Exceptions  : none
  Caller      : internal
  Status      : At Risk
              : under development

=cut

sub read_from_file {