#!/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]+)}{$1}g;
$pred =~ s{([E]+)}{$1}g;
if ($out) {
open(my $OUT, ">$out") or die "$out: $!";
select($OUT);
}
my $html = '
Simple JNet Output