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run_pretty.pl
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run_pretty.pl
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use strict;
use warnings;
$| = 1;
use RNAOpt::RNAfold::Worker;
use RNAOpt::Runner;
use JSON;
use PostScript::Convert;
use Template;
use IPC::Open3;
use File::Copy;
my $RELPLOT = 'perl /usr/local/share/ViennaRNA/bin/relplot.pl';
my $RNAPLOT = 'RNAplot -t1';
open(ANTISENSE, '<', 'antisense.txt') or die 'No antisense.txt!';
open(INDEXFILE, '>', 'index.html') or die "Couldn't open index.html!";
mkdir './img';
mkdir './plot';
my $REPORT = 25;
my @sequences = <ANTISENSE>;
chomp @sequences;
# not a nice way but it works
@sequences = map(uc, @sequences);
foreach(@sequences) { s/[^ACGU<>\[\]]//g; }
sub result_hook {
my $result = shift;
store_plot($result);
print '.';
};
my $worker = RNAOpt::RNAfold::Worker->new();
my $runner = RNAOpt::Runner->new(
rnafold_worker => $worker,
tagged_sequences => \@sequences,
hook => \&result_hook,
);
print "Setup complete: will generate a report for top $REPORT sequences.\n";
print "Generating structures";
my $results = $runner->results;
print "Done.\n";
my @sorted_results = sort { ($b->region_clear_ratio_centroid + $b->region_clear_ratio_mfe) cmp ($a->region_clear_ratio_centroid + $a->region_clear_ratio_mfe) } @{$results};
# Generate the report
my $template_html = <<"ENDHTML";
<!DOCTYPE html>
<html>
<head>
<title>Results!</title>
<link rel="stylesheet" href="http://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
<style>
.seq { font-size: 9px; }
.region { background-color: #AAF; }
.site { background-color: #F88; }
</style>
</head>
<body>
<div class="container-fluid">
<div class="row">
<div class="col-xs-12">
<h1>Report for [% title %]</h1>
</div>
</div>
[% FOREACH result IN results %]
<div class="row">
<div class="col-xs-12">
<table class="table">
<thead>
<tr>
<th>Rank</th>
<th>MFE</th>
<th>Region Clarity (MFE)</th>
<th>Region Clarity (Centroid)</th>
<th>Site Clear? (MFE)</th>
<th>Site Clear? (Centroid)</th>
<th>Length</th>
</tr>
</thead>
<tbody>
<tr>
<td>[% result.rank %]</td>
<td>[% result.mfe %] kcal/mol</td>
<td>[% result.region_clarity_mfe %]%</td>
<td>[% result.region_clarity_centroid %]%</td>
<td>[% result.site_clear_mfe %]</td>
<td>[% result.site_clear_centroid %]</td>
<td>[% result.length %]</td>
</tr>
</tbody>
</table>
</div>
<div class="col-xs-12">
<table class="table">
<thead>
<tr>
<th>Sequence / Structure (MFE) / Structure (Centroid)</th>
</tr>
</thead>
<tbody>
<tr>
<td><samp class="seq">[% result.sequence_l %]<span class="region">[% result.sequence_rl %]<span class="site">[% result.sequence_s %]</span>[% result.sequence_rr %]</span>[% result.sequence_r %]</td>
</tr>
<tr>
<td><samp class="seq">[% result.structure_mfe_l %]<span class="region">[% result.structure_mfe_rl %]<span class="site">[% result.structure_mfe_s %]</span>[% result.structure_mfe_rr %]</span>[% result.structure_mfe_r %]</td>
</tr>
<tr>
<td><samp class="seq">[% result.structure_centroid_l %]<span class="region">[% result.structure_centroid_rl %]<span class="site">[% result.structure_centroid_s %]</span>[% result.structure_centroid_rr %]</span>[% result.structure_centroid_r %]</td>
</tr>
</tbody>
</table>
</div>
<div class="col-xs-12 col-md-6">
MFE:
<img class="img-responsive" src="[% result.image_path_mfe %]"></img>
</div>
<div class="col-xs-12 col-md-6">
Centroid:
<img class="img-responsive" src="[% result.image_path_centroid %]"></img>
</div>
</div>
[% END %]
</div>
<script src="http://code.jquery.com/jquery-2.1.1.min.js"></script>
<script src="http://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
</body>
</html>
ENDHTML
sub generate_result_view_hash {
my $rank = shift;
my $result = shift;
my %view = ();
$view{rank} = $rank;
$view{mfe} = $result->mfe;
$view{region_clarity_mfe} = sprintf '%.1f', $result->region_clear_ratio_mfe()*100.0;
$view{region_clarity_centroid} = sprintf '%.1f', $result->region_clear_ratio_centroid()*100.0;
$view{site_clear_mfe} = $result->site_clear_mfe ? 'Yes' : 'No';
$view{site_clear_centroid} = $result->site_clear_centroid ? 'Yes' : 'No';
$view{'length'} = length $result->sequence_raw;
sub areas {
my $result = shift;
my $s = shift;
my ($rf, $rl, $sf, $sl) = ($result->region_first, $result->region_last, $result->site_first, $result->site_last);
my @res = (
substr($s, 0, $rf),
substr($s, $rf, $sf - $rf),
substr($s, $sf, $sl + 1 - $sf),
substr($s, $sl + 1, $rl - $sl),
substr($s, $rl + 1),
);
return \@res;
}
@view{('sequence_l', 'sequence_rl', 'sequence_s', 'sequence_rr', 'sequence_r')} = @{ areas($result, $result->sequence_raw) };
@view{('structure_mfe_l', 'structure_mfe_rl', 'structure_mfe_s', 'structure_mfe_rr', 'structure_mfe_r')} = @{ areas($result, $result->structure_mfe) };
@view{('structure_centroid_l', 'structure_centroid_rl', 'structure_centroid_s', 'structure_centroid_rr', 'structure_centroid_r')} = @{ areas($result, $result->structure_centroid) };
$view{image_path_mfe} = 'img/'.$rank.'/mfe.png';
$view{image_path_centroid} = 'img/'.$rank.'/centroid.png';
return \%view;
};
sub store_plot {
my $result = shift;
my $seq = $result->sequence_raw;
mkdir "plot/$seq";
move('rna.ps', "plot/$seq/rna_mfe.ps");
move('dot.ps', "plot/$seq/dot_mfe.ps");
move('dot2.ps', "plot/$seq/dot_centroid.ps");
}
my $template = Template->new();
my $output = '';
my @results_for_display = ();
foreach my $rank (0..$REPORT) {
push @results_for_display, generate_result_view_hash($rank, $sorted_results[$rank]);
}
print "Generating images";
# Generate the plots for each of them
foreach my $rank (0..$REPORT) {
my $result = $sorted_results[$rank];
my ($rnaplot_in, $rnaplot_out);
my $pid = open3($rnaplot_in, $rnaplot_out, $rnaplot_out, $RNAPLOT) or die 'Cannot open RNAplot!';
print $rnaplot_in $result->sequence_raw."\n";
print $rnaplot_in $result->structure_centroid."\n";
close $rnaplot_in;
waitpid $pid, 0; # wait for RNAplot it to finish
my $seq = $result->sequence_raw;
move('rna.ps', "plot/$seq/rna_centroid.ps");
# Now to generate the coloured plots, thanks to the RELPLOT utility
system("$RELPLOT plot/$seq/rna_mfe.ps plot/$seq/dot_mfe.ps > plot/$seq/coloured_mfe.ps");
system("$RELPLOT plot/$seq/rna_centroid.ps plot/$seq/dot_centroid.ps > plot/$seq/coloured_centroid.ps");
mkdir "img/$rank";
psconvert("plot/$seq/coloured_mfe.ps", "img/$rank/mfe.png", paper_size => [ 452, 552 ]);
psconvert("plot/$seq/coloured_centroid.ps", "img/$rank/centroid.png", paper_size => [ 452, 552 ]);
# well that took a lot!
print '.';
}
print "Done.\n";
print "Complete! Report in index.html!\n";
$template->process(
\$template_html,
{ 'results' => \@results_for_display, 'title' => $ARGV[0] },
\$output,
) || die $template->error();
print INDEXFILE $output;