fold.html

% if ($mfe_method or $input_fasta or $fold_sequence) {

<%perl>
my $tempfile_fh = new File::Temp(SUFFIX => ".fasta", DIR => "$ENV{PRFDB_HOME}/folds", UNLINK=>0);
my $new_filename = $tempfile_fh->filename();
use File::Basename;
my $short_filename = basename($new_filename);
my $contents;
if ($input_fasta) {
 use Apache2::Upload;
 my $req = new Apache2::Request($r);
 my $upload = $req->upload("input_fasta");
 my $upload_filename = $upload->filename();
 my $size = $upload->slurp($contents);
} elsif ($fold_sequence) {
 $contents =  ">${short_filename}
${fold_sequence}
";
}
unless ($contents) {
  print "<p>No input.</p>\n";
  return;
}

$contents = lc($contents);
$contents =~ s/t/u/g;

print $tempfile_fh $contents;
close $tempfile_fh;

print "<pre>
$contents
</pre>\n";
my $new_url = "folds/$short_filename.html";


use Proc::Forkfunc;
my @child_args = ($config, $short_filename, $mfe_method, $num_refreshes);
forkfunc(\&tmp_fold, @child_args);


sub tmp_fold {
  my $config = shift;
  my $new_filename = shift;
  my $function = shift;
  my $refreshes = shift;
  my $input_path = "$ENV{PRFDB_HOME}/folds/$new_filename";
  my $fold = new RNAFolders(config => $config, file => $input_path, genome_id => 0, species => 'saccharomyces_cerevisiae', accession => 2, start => 0,);
  my $mfe_info;
  if ($function eq 'nupack') {
    $mfe_info = $fold->Nupack_NOPAIRS();
  }  elsif ($function eq 'pknots') {
    $mfe_info = $fold->Pknots('nopseudo');
  } elsif ($function eq 'hotknots') {
    $mfe_info = $fold->Hotknots(chdir => qq"$ENV{PRFDB_HOME}/folds");
  } elsif ($function eq 'rnafold') {
    $mfe_info = $fold->Vienna();
  } elsif ($function eq 'pknots_pseudo') {
    $mfe_info = $fold->Pknots();
  } elsif ($function eq 'ilm') {
    $mfe_info = $fold->ILM();
  } elsif ($function eq 'unafold') {
    $mfe_info = $fold->Unafold();
  } else {
    $mfe_info = $fold->Multiple(['hotknots','nupack','pknots']);
  }

  my $mfe = $mfe_info->{mfe};
  my $parsed = $mfe_info->{parsed};
  my $barcode = $mfe_info->{barcode};
  my $output = $mfe_info->{output};
  my $pairs = $mfe_info->{pairs};
  my $sequence = $mfe_info->{sequence};
  my $parens = $mfe_info->{parens};
  my $bpseq_string = $fold->Make_ct(sequence => $sequence, output => $output, function => $function);
  my $turner = $fold->Compute_Energy(sequence => $sequence, parens => $parens);
  open(BPSEQ_FILE, ">${input_path}.ct");
  print BPSEQ_FILE $bpseq_string;
  close(BPSEQ_FILE);
  my $pic_output = "$ENV{PRFDB_HOME}/folds/$new_filename.svg";
  my $pictures = new PRFGraph(sequence=>$sequence, parsed => $parsed, output => $output);
  my $dimensions = $pictures->Make_Feynman($pic_output, 0);


  my $jviz_type = 'jviz_classic_structure';
  my $jviz_url_string = '';
  my $jviz_pic_output = $pic_output;
  $jviz_pic_output =~ s/\.svg/-${jviz_type}\.png/g;
  $jviz_pic_output =~ s/jviz_//g;
#  $jviz_pic_output =~ s/\.fasta/\.bpseq/g;

  my $jviz_pic_input = $pic_output;
  $jviz_pic_input =~ s/\.svg//g;

#  print STDERR "INFO: $jviz_pic_input $jviz_pic_output\n";
#  my $jviz_output = $pictures->jViz(input_filename => "${jviz_pic_input}.ct", debug => 0, jviz_type => $jviz_type, output_filename => $jviz_pic_output);
  my $jviz_output = $pictures->jViz(mfe_id => undef,
                                    input_file => "${jviz_pic_input}.ct",
				    debug => 0, 
				    jviz_type => $jviz_type,
				     output_file => $jviz_pic_output);

#  my $mangle = $jviz_pic_input;
#  $mangle =~ s/\.fasta/\.fasta-classic_structure\.png/g;
#  my $cmd = qq"cp $jviz_output->{filename} $mangle";
#  system($cmd);
  my $url_file = basename($jviz_pic_output);
  $jviz_url_string .= "<center><img src=\"$url_file\"><br>\n";
  $jviz_url_string .= "</center>";

  open (HANDLE, ">$input_path.html") or Callstack(message => "Cannot open HANDLE $new_filename.html");
  print HANDLE qq(The minimum free using $function energy is: $mfe (Turner99: $turner)<br>
<pre>
$sequence
$parens
</pre><br>
<embed id=\"feynman\" src=\"$new_filename.svg\" align=\"bottom\"></embed>
<br>
$jviz_url_string
<br>
Download <a href=\"/download/svg2something.html?format=png&input=/folds/${new_filename}.svg\">png</a> or <a href=\"/download/svg2something.html?format=ps&intput=/folds/${new_filename}.svg\">ps</a> or  <a href=\"/download/svg2something.html?format=pdf&intput=/folds/${new_filename}.svg\">pdf</a>
<br>
  );  ## This marks the end of the printed html fragment of the output
  close(HANDLE);
}

</%perl>

<p>This will redirect you to the output page for your folding in 5 seconds.<br>
Keep in mind that these programs take exponentially more time with respect to length of query sequence.
For example:<br>
If you use pknots with pseudoknots and a 60 nt sequence, it should take 5 seconds or less,<br>
but 80 nt will take about 10 seconds, 90 nt will take 4 minutes, 100 nt will take 1.5 hours.<br>
Nupack and a 60 nt sequence takes about 0.5 seconds, 90 nt takes 5 seconds, 100 nt takes 4 minutes.<br>
RNAfold and 60 nt takes about 0.1 second, 90 nt takes 1 second, 150 nt takes 10 seconds, 180 nt takes 2 hours...
</p>
<& /js/refresh.html, refresh_url => "/folds/${short_filename}.html", seconds => 5 &>
<script>  
  function load() {  
  }  
  window.onload = mydoLoad;  
</script>

% } else {

<FORM action="fold.html" enctype="multipart/form-data" method="POST">
Use this form to fold a _short_ sequence.<br>

Choose a fasta formatted file: 
<input type="file" name="input_fasta"><br>
Or input some sequence below:<br>
<textarea name="fold_sequence" rows=5 cols=80></textarea><br>
and Fold it with:
<select name="mfe_method">
<option selected="selected" value="nupack">Nupack</option>
<option value="pknots">Pknots</option>
<option value="pknots_pseudo">Pknots with pseudoknots</option>
<option value="hotknots">HotKnots</option>
<option value="rnafold">RNAfold</option>
<option value="unafold">UNAfold</option>
<option value="all">all</option>
</select><br>
<input type="submit" name="fold submit" value="Fold"><br>


</form>

% }

<%init>
  my $tempfile;
  my $new_filename;
</%init>

<%args>
  $fold_sequence => undef
  $mfe_method => undef
  $input_fasta => undef
  $num_refreshes => 0
</%args>