make_distribution.html

Generating distribution for <% $species %>
<%perl>
my $cloud = new PRFGraph(config => $config);
my $pknots_only = undef;
my $boot_table = "boot_$species";
my $suffix = undef;
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}";
}
$suffix .= "-${seqlength}";
my $cloud_output_filename = $cloud->Picture_Filename(type => 'cloud', species => $species, suffix => $suffix,);
my $cloud_url = $cloud->Picture_Filename(type => 'cloud', species => $species, url => 'url', suffix => $suffix,);
$cloud_url = $ENV{PRFDB_HOME} . '/' . $cloud_url;
my ($points, $averages);
my $mt = "mfe_$species";
if (!-f $cloud_output_filename) {
  $points = $db->Collect_Cloud(species => $species, seqlength => $seqlength, filters => \@filters);
}
  $points_stmt = qq"SELECT $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 ";
  $averages_stmt = qq"SELECT avg($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 = $vars->{seqlength} AND $mt.id = $boot_table.mfe_id 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;
  $points = $db->MySelect(statement => $points_stmt, vars => [$species]);
  $averages = $db->MySelect(statement => $averages_stmt, vars => [$species], type => 'row',);
  #    }
  my $cloud_data;
  my %args;
  if (defined($pknots_only)) {
    %args = (seqlength => $seqlength,
	     species => $species,
	     points => $points,
	     averages => $averages,
	     filename => $cloud_output_filename,
	     url => $ENV{PRFDB_HOME},
	     pknot => 1,
	     slipsites => $slipsites
	    );
  }
  else {
    %args = (
	     seqlength => $seqlength,
	     species => $species,
	     points => $points,
	     averages => $averages,
	     filename => $cloud_output_filename,
	     url => $ENV{PRFDB_HOME},
	     slipsites => $slipsites,
	    );
  }
  $cloud_data = $cloud->Make_Cloud(%args);
}
if ($slipsites ne 'all') {
  $vars->{slipsites} = $slipsites;
}
$vars->{map_url} = "$vars->{cloud_url}" . '.map';
$vars->{map_file} = "$vars->{cloud_file}" . '.map';

my $extension_percent_filename = $cloud->Picture_Filename(type => 'extension_percent', species => $species,);
my $extension_codons_filename = $cloud->Picture_Filename(type=> 'extension_codons', species => $species,);
$vars->{percent_map_file} = $extension_percent_filename . '.map';
$vars->{codons_map_file} = $extension_codons_filename . '.map';

if (!-f $extension_codons_filename) {
  $cloud->Make_Extension($species, $extension_codons_filename, 'codons', $ENV{PRFDB_HOME});
}
if (!-f $extension_percent_filename) {
  $cloud->Make_Extension($species, $extension_percent_filename, 'percent', $ENV{PRFDB_HOME});
}
my $bargraphs = qq"$ENV{PRFDB_HOME}/images/cloud/$species/cloud-bar-percentsig.png";
if (!-f $bargraphs) {
  my $cloud_data = $cloud->Make_Cloud(seqlength => $seqlength, species => $species, points => $points,
	averages => $averages, filename => qq"$ENV{PRFDB_HOME}/images/cloud/$species/cloud-all-AAAAAAA-100.png",
	url => $ENV{PRFDB_HOME}, slipsites => 'AAAAAAA',);
}
</%perl>

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