--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/External/TMHMM.pm	Mon Jun 05 02:51:26 2023 +0000
@@ -0,0 +1,164 @@
+package CPT::External::TMHMM;
+no warnings;
+use Moose;
+use File::Temp qw(tempfile);
+use IPC::Run qw(run);
+use File::Temp qw(tempdir);
+use File::Copy qw(move);
+
+has 'sequence' => ( is => 'rw', isa => 'Str' );
+has 'response' => ( is => 'rw', isa => 'Str' );
+
+has 'num_predicted'       => ( is => 'rw', isa => 'Int' );
+has 'predicted_locations' => ( is => 'rw', isa => 'ArrayRef' );
+has 'prob_n_in'           => ( is => 'rw', isa => 'Str' );
+has 'hash'                => ( is => 'rw', isa => 'Str' );
+has 'picture_location'    => ( is => 'rw', isa => 'Str' );
+
+my ( $fh, $filename, $image );
+
+sub create_fasta_file {
+	my ( $self, $seq ) = @_;
+	( $fh, $filename ) = tempfile( "cpt.tmhmm.XXXXXXX", UNLINK => 1 );
+
+	#printf $fh ">%s\n%s\n", 'seq', $seq;
+	printf $fh "%s\n", $seq;
+	return $filename;
+}
+
+sub parse_text {
+	my ($self) = @_;
+	unless ( $self->predicted_locations() ) {
+		$self->predicted_locations( [] );
+	}
+	unless ( $self->num_predicted() ) {
+		$self->num_predicted(0);
+	}
+	foreach my $line ( split( /\n/, $self->response() ) ) {
+		if ( $line =~ /Number of predicted TMHs:\s*(\d+)/ ) {
+			$self->num_predicted($1);
+		}
+		elsif ( $line =~ /Total prob of N-in:\s*([0-9.]*)/ ) {
+			$self->prob_n_in($1);
+		}
+		elsif ( $line =~ /TMHMM2.0\s*TMhelix\s*([0-9]+)\s*([0-9]+)/ ) {
+
+			#$self->num_predicted($self->num_predicted()+1);
+			push( @{ $self->predicted_locations() }, [ $1, $2 ] );
+		}
+	}
+
+	#	# seq Length: 145
+	#	# seq Number of predicted TMHs:  1
+	#	# seq Exp number of AAs in TMHs: 20.91302
+	#	# seq Exp number, first 60 AAs:  20.91265
+	#	# seq Total prob of N-in:        0.04659
+	#	# seq POSSIBLE N-term signal sequence
+	#	seq	TMHMM2.0	outside	     1     3
+	#	seq	TMHMM2.0	TMhelix	     4    23
+	#	seq	TMHMM2.0	inside	    24   145
+}
+
+sub analyze {
+	my ( $self, $seq ) = @_;
+
+	# Set our hash
+	require Digest::MD5;
+	$self->hash( Digest::MD5::md5_hex($seq) );
+
+	# Set our sequence
+	$self->sequence($seq);
+
+	# Tmp dir to run in
+	my $dir = tempdir( CLEANUP => 1 );
+	my $tmpfile = $self->create_fasta_file($seq);
+
+	# Plot and use specified workdir
+	my @cmd = ( 'tmhmm.pl', '-plot', '-workdir', $dir, '<', $tmpfile );
+
+	# Run the command
+	my ( $in, $out, $err );
+	run \@cmd, \$in, \$out, \$err;
+
+	# If error,we error
+	if ($err) {
+
+		# print STDERR "Error: $err\n";
+		# Kinda a crappy way to handle this...
+		$self->response($err);
+		return 0;
+	}
+	{
+
+		# Move the created plot to a known location
+		my @tmhmm_files = glob("$dir/*/*.png");
+
+		# There's really only one png but this is just as easy to write
+		for my $png (@tmhmm_files) {
+			$image = sprintf( "/tmp/cpt.ext.tmhmm.%s.png", $self->hash() );
+			move( $png, $image );
+		}
+
+		# Module to remove the temporary dir so we clean up after
+		# ourselves quickly, since this programme seems to open a LARGE
+		# number of file handles.
+		require File::Path;
+		File::Path::remove_tree($dir);
+
+		# set response and parse it, then return OK.
+		$self->response($out);
+		$self->parse_text();
+		return 1;
+	}
+}
+
+sub cleanup {
+	if ( defined($fh) ) {
+		close($fh);
+		unlink($filename);
+		if ( -e $image ) {
+			unlink($image);
+		}
+	}
+}
+
+END {
+	if ( defined($fh) ) {
+		close($fh);
+		unlink($filename);
+		if ( -e $image ) {
+			unlink($image);
+		}
+	}
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::External::TMHMM
+
+=head1 VERSION
+
+version 1.99.4
+
+=head1 AUTHOR
+
+Eric Rasche <rasche.eric@yandex.ru>
+
+=head1 COPYRIGHT AND LICENSE
+
+This software is Copyright (c) 2014 by Eric Rasche.
+
+This is free software, licensed under:
+
+  The GNU General Public License, Version 3, June 2007
+
+=cut