X-Git-Url: http://source.jalview.org/gitweb/?p=jpred.git;a=blobdiff_plain;f=websoft%2Fbin%2Fconcise2simplehtml;fp=websoft%2Fbin%2Fconcise2simplehtml;h=fbdc770daca7666ca9e11703d34dba11320eff75;hp=0000000000000000000000000000000000000000;hb=443c228bf0712d71e7fa34b5a2dc4b2b2e79f13f;hpb=9aa768067094f24f46f273077f867348e6143711
diff --git a/websoft/bin/concise2simplehtml b/websoft/bin/concise2simplehtml
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+#!/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
+
+