--- /dev/null
+#!/usr/bin/perl
+
+## CC 18/05/2006
+# New version of script as the original (OO perl) version
+# doesn't work on the new cluster. As it's a very simple
+# parser it can be easily re-implemented
+
+use strict;
+use warnings;
+use Getopt::Long;
+use Jpred;
+
+my $file;
+my $out;
+
+GetOptions(
+ 'file=s' => \$file,
+ 'out=s' => \$out
+) or die $!;
+
+$file or die "no --file argument\n";
+
+open(my $FH, $file) or die "$!";
+my $query;
+my $pred;
+while(<$FH>) {
+ # jnet concise file is a series of outputs preceeded by
+ # a definition separated by ':' on each line e.g.:
+ #
+ # align1;QUERY:M,F,L,A,Q,E,I,I,R,K,K,R,D,G,H,A,L,S,D,E,E,I,...,
+ # jpred:-,-,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,H,H,H,H,H,H,H,...,
+ #
+ # Find the two lines above and extract the query sequence and the
+ # jpred prediction.
+
+ chomp;
+
+ my ($def, $data) = split /:/, $_ or next;
+
+ if ($def eq 'jnetpred') {
+ $pred = $data;
+ $pred =~ s/\,//g; # remove all the ',' in prediction
+ }
+ if ($def =~ /align1/) {
+ next if $query; # skip any hits to align1x sequences. We only want the 1st hit.
+ $query = $data;
+ $query =~ s/\,//g; # remove all ',' in sequence
+ }
+}
+close($FH);
+if (!$query || !$pred) {
+ die "no jpred output or query sequence found in $file";
+}
+
+# colour the predictions
+$pred =~ s{([H]+)}{<font color="#e90055">$1</font>}g;
+$pred =~ s{([E]+)}{<font color="#ffa800">$1</font>}g;
+
+if ($out) {
+ open(my $OUT, ">$out") or die "$out: $!";
+ select($OUT);
+}
+
+
+my $html = '<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html lang="en-GB" xml:lang="en-GB">
+<head><title>Simple JNet Output</title>
+<link rel="stylesheet" type="text/css" href="http:/webservices:12345/jpred.css" />
+</head><body><pre><code>';
+$html .= "$query\n";
+$html .= "$pred\n";
+$html .= "</code></pre>
+$JPREDFOOT</body></html>";
+print $html;
+
+exit;
+
git://source.jalview.org / jpred.git / blobdiff