generate_distribution.html

<%perl>

sub tmp_cloud {
  my $config = shift;
  my $filters = shift;
  my $species = shift;
  my $slipsites = shift;
  my $mfe_methods = shift;
  my $seqlength = shift;
  my $cloud = new PRFGraph(config=>$config);
  my $suffix;
  my $pknots_only;
  foreach my $filter (@$filters) {
   if ($filter eq 'pseudoknots only') {
    $suffix .= "-pknot";
    $pknots_only = 1;
   } elsif ($filter eq 'coding sequence only') {
    $suffix .= "-cs";
   }
  }
  if ($slipsites eq 'all') {
   $suffix .= "-all";
  } else {
   $suffix .= "-${slipsites}";
  }
  $suffix .= "-${mfe_methods}-${seqlength}";
  my $cloud_output_filename = $cloud->Picture_Filename(type => 'cloud', species => $species, mfe_methods => $mfe_methods, suffix => $suffix,);
  my $cloud_url = $cloud->Picture_Filename(type => 'cloud', species => $species, url => 'url', mfe_methods => $mfe_methods, suffix => $suffix,);
  my $boot_table = "boot_$species";
  my $mt = "mfe_$species";
  my $points_stmt = qq"SELECT SQL_BUFFER_RESULT $mt.mfe, $boot_table.zscore, $mt.accession, $mt.knotp, $mt.slipsite, $mt.start, genome.genename FROM $mt, $boot_table, genome WHERE $boot_table.zscore IS NOT NULL AND $mt.mfe > -80 AND $mt.mfe < 5 AND $boot_table.zscore > -10 AND $boot_table.zscore < 10 AND $mt.seqlength = $seqlength AND $mt.id = $boot_table.mfe_id AND ";
  my $averages_stmt = qq"SELECT SQL_BUFFER_RESULT avg($mt.mfe), avg($boot_table.zscore), stddev($mt.mfe), stddev($boot_table.zscore) FROM $mt, $boot_table WHERE $boot_table.zscore IS NOT NULL AND $mt.mfe > -80 AND $mt.mfe < 5 AND $boot_table.zscore > -10 AND $boot_table.zscore < 10 AND $mt.seqlength = $seqlength AND $mt.id = $boot_table.mfe_id AND ";

  if ($mfe_methods ne 'all') {
    if ($mfe_methods eq 'nupack+hotknots') {
        $points_stmt .= "( $mt.mfe_method = 'nupack' OR $mt.mfe_method = 'hotknots' ) AND ";
	$averages_stmt .= "( $mt.mfe_method = 'nupack' OR $mt.mfe_method = 'hotknots' ) AND ";
    } elsif ($mfe_methods eq 'nupack') {
        $points_stmt .= "$mt.mfe_method = 'nupack' AND ";
	$averages_stmt .= "$mt.mfe_method = 'nupack' AND ";
    } elsif ($mfe_methods eq 'pknots') {
        $points_stmt .= "$mt.mfe_method = 'pknots' AND ";
	$averages_stmt .= "$mt.mfe_method = 'pknots' AND ";
    } elsif ($mfe_methods eq 'hotknots') {
        $points_stmt .= "$mt.mfe_method = 'hotknots' AND ";
	$averages_stmt .= "$mt.mfe_method = 'hotknots' AND ";
    }
  }

  foreach my $filter (@${filters}) {
   if ($filter eq 'pseudoknots only') {
    $points_stmt .= "$mt.knotp = '1' AND ";
    $averages_stmt .= "$mt.knotp = '1' AND ";
   } elsif ($filter eq 'coding sequence only') {
    $points_stmt .= "";
    $averages_stmt .= "";
   }
  }
  $points_stmt .= " $mt.genome_id = genome.id";
  $averages_stmt =~ s/AND $//g;
  my $points = $db->MySelect(statement => $points_stmt,);
  my $averages = $db->MySelect(statement => $averages_stmt, type => 'row');
  my %args;
  if (defined($pknots_only)) {
    %args = (
	seqlength => $seqlength,
	species => $species,
	points => $points,
	mfe_methods => $mfe_methods,
	averages => $averages,
	filename => $cloud_output_filename,
	url => $ENV{PRFDB_HOME},
	pknot => 1,
	slipsites => $slipsites
	);
   } else {
    %args = (
	seqlength => $seqlength,
	species => $species,
	points => $points,
	averages => $averages,
	mfe_methods => $mfe_methods,
	filename => $cloud_output_filename,
	url => $ENV{PRFDB_HOME},
	slipsites => $slipsites,
       );
    }
    my $cloud_data = $cloud->Make_Cloud(%args);
}
  use Proc::Forkfunc;
  my @child_args = ($config, $filters, $species, $slipsites, $mfe_methods, $seqlength);
  forkfunc(\&tmp_cloud,@child_args);
</%perl>

<%args>
  $species => "saccharomyces_cerevisiae"
  $mfe_methods => "all"
  $seqlength => 100
  $slipsites => "all"
  $filters => undef
</%args>