Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / HMMER / Profile.pm

diff --git a/binaries/src/jpred/lib/HMMER/Profile.pm b/binaries/src/jpred/lib/HMMER/Profile.pm
new file mode 100644 (file)
index 0000000..19e7085
--- /dev/null
+++ b/binaries/src/jpred/lib/HMMER/Profile.pm
@@ -0,0 +1,102 @@
+package HMMER::Profile;
+
+use strict;
+use warnings;
+use Carp;
+use base qw(Root Read Write);
+
+sub read {
+       my ($self, $fh) = @_;
+
+       local $/ = "\n";
+
+       my ($flag, @data) = 0;
+       while (my $line = <$fh>) {
+               $flag = 1, next if $line =~ /^Cons/;
+               next unless $flag;
+               next if $line =~ /^! \d+/;
+               last if $line =~ /^ \*/;
+
+               chomp $line;
+               $line =~ s/^\s*//g;
+               #$self->seq($self->seq, [ (split / +/, $line)[1..24] ]);
+
+               $self->add_line((split /\s+/, $line)[1..24]);
+       }
+}
+
+sub write {
+       my ($self, $fh) = @_;
+       for ($self->get_line) {
+               print join(" ", @{ $_}) , "\n";
+               exit;
+               #print join(" ", map { @{ $_ }), "\n";
+               print $fh join(" ", map { sprintf "%.5f", $_ } @{ $_ }), "\n";
+       }
+}
+
+sub add_line {
+       my $self = shift;
+       @_ or croak "No data passed to HMMER::Profile::add_line";
+       push @{ $self->{__PACKAGE__."lines"} }, pack "d*", @_;
+}
+
+sub get_line {
+       my ($self, $line) = @_;
+
+       if (defined $line) { return [ unpack "d*", ${$self->{__PACKAGE__."lines"}}[$line] ] }
+       else {
+               return map { [ unpack "d*", $_ ] } @{$self->{__PACKAGE__."lines"}}
+       }
+}
+
+1;
+__END__
+
+=head1 NAME
+
+HMMER::Profile - Convert the output of hmmconvert to a profile for Jnet
+
+=head1 EXAMPLE
+
+system("hmmconvert -p hmmer.model hmmer.prf");
+
+my $prof = HMMER::Profile->new;
+$prof->read_file("hmmer.prf");
+
+my @data = $prof->jnet
+print join(" ", @{$_}), "\n" for @data;
+
+=head1 DESCRIPTION
+
+Takes the output of the HMMER program hmmconvert with the -p option and calculates the profile used by Jpred to calculate secondary structure.
+
+=head1 METHODS
+
+=head2 my $prof = HMMER::Profile->new;
+
+Create a new object.
+
+=head2 $prof->read_file("path_to_hmmer_model_converted_to_prf");
+
+Read a HMMER model that's been converted to PRF format via the HMMER hmmconvert program with the -p option.
+
+=head2 my @data = $prof->seq
+
+Returns an array of array refs of the HMMER numbers.
+
+=head2 my @data = $prof->jnet
+
+Returns an array of array refs of frequences for use in Jnet.
+
+=head1 SEE ALSO
+
+Packages Root, Read and Sequence.
+
+=head1 BUGS
+
+The whole set of profile modules is a bit of an abortion now, as there is no standard interface and the methods do different things for different objects. Converting the different representations is a nightmare because of this.
+
+=head1 AUTHOR
+
+Jonathan Barber <jon@compbio.dundee.ac.uk>