--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/External/LipoP.pm	Mon Jun 05 02:48:47 2023 +0000
@@ -0,0 +1,92 @@
+package CPT::External::LipoP;
+no warnings;
+use Moose;
+use File::Temp qw(tempfile);
+use IPC::Run qw(run);
+
+has 'sequence' => ( is => 'rw', isa => 'Str' );
+has 'response' => ( is => 'rw', isa => 'Str' );
+has 'cleavage' => ( is => 'rw', isa => 'ArrayRef' );
+has 'tmpfile' => (is => 'rw', isa => 'Any');
+
+sub create_fasta_file {
+	my ( $self, $seq ) = @_;
+	my ( $fh, $filename ) = tempfile( "cpt.lipop.XXXXXXX", UNLINK => 1 );
+
+	#printf $fh ">%s\n%s\n", 'seq', $seq;
+	printf $fh "%s\n", $seq;
+	close($fh);
+	return $filename;
+}
+
+sub parse_text {
+	my ($self) = @_;
+
+	foreach my $line ( split( /\n/, $self->response() ) ) {
+		if ( $line =~ /#.*cleavage=(\d+)-(\d+)/ ) {
+			$self->cleavage( [ $1, $2 ] );
+		}
+	}
+	#	# seq SpII score=17.8897 margin=13.48964 cleavage=19-20 Pos+2=K
+	#	# Cut-off=-3
+	#	seq	LipoP1.0:Best	SpII	1	1	17.8897
+	#	seq	LipoP1.0:Margin	SpII	1	1	13.48964
+	#	seq	LipoP1.0:Class	SpI	1	1	4.40006
+	#	seq	LipoP1.0:Class	CYT	1	1	-0.200913
+	#	seq	LipoP1.0:Signal	CleavII	19	20	17.8897	# LVVSA|CKSPP Pos+2=K
+	#	seq	LipoP1.0:Signal	CleavI	28	29	4.03409	# PPVQS|QRPEP
+	#	seq	LipoP1.0:Signal	CleavI	21	22	2.04071	# VSACK|SPPPV
+	#	seq	LipoP1.0:Signal	CleavI	27	28	-2.07502	# PPPVQ|SQRPE
+	#	seq	LipoP1.0:Signal	CleavI	19	20	-2.6907	# LVVSA|CKSPP
+	#	seq	LipoP1.0:Signal	CleavI	22	23	-2.87659	# SACKS|PPPVQ
+}
+
+sub analyze {
+	my ( $self, $seq ) = @_;
+	$self->sequence($seq);
+	$self->tmpfile($self->create_fasta_file($seq));
+	my @cmd = ( 'LipoP', $self->tmpfile(), '-workdir', '/tmp/nonexistant/', '-wwwdir', '/tmp/nonexistant' );
+	my ( $in, $out, $err );
+	run \@cmd, \$in, \$out, \$err;
+	if ($err) { print "Error: $err\n"; }
+	$self->response($out);
+	$self->parse_text();
+	unlink($self->tmpfile());
+}
+
+sub cleanup {
+	my ($self) = @_;
+	return;
+}
+
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::External::LipoP
+
+=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