--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/Bio/SAR.pm	Mon Jun 05 02:50:07 2023 +0000
@@ -0,0 +1,76 @@
+package CPT::Bio::SAR;
+use strict;
+use warnings;
+use autodie;
+use Moose;
+
+sub filter_sar {
+	my ($self, @seqs) = @_;
+	my @good;
+	foreach(@seqs){
+		if(has_sar_motif($_)){
+			push(@good, $_);
+		}
+	}
+	return @good;
+}
+
+sub has_sar_motif {
+	my ( $self, $seq ) = @_;
+	
+	return 0 if(length $seq < 40);
+	
+	my $reg_a = qr/([^DEKR]{3}K[^DEKR]{8,}[^DER]{1}[^DEKR]{3})/;
+	my $reg_b = qr/([KR]{1,}[^DEKR]{12,}[^DER]{1}[^DEKR]{3})/;
+
+	my $first40 = substr( $seq, 0, 40 );
+
+	# there is a transmembrane domain in the first 40 AAs
+	# there is at least one positive charged AAs in front of the TMD
+	if ( $first40 =~ $reg_a || $first40 =~ $reg_b ) {
+		my $modi1st40 = $first40;
+			# Cut out the match, and then add the whole thing to the end.
+		my $t4homology =
+			#substr($seq,0, $-[0] ), # Before the match
+			#substr($seq, $-[0], ($+[0] - $-[0])), # the match
+			substr($seq, $+[0]). # After the match
+			$first40;
+		$t4homology = substr($t4homology, 0 , 40);
+
+		if ( $t4homology =~ qr/E[A-Z]{8}[DC][A-Z]{4,5}T/ ) {
+			return 1;
+		}
+	}
+	return 0;
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Bio::SAR
+
+=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