--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_psm_prep/lib/CPT/Bio/Lipo.pm	Tue Jul 05 05:38:34 2022 +0000
@@ -0,0 +1,85 @@
+package CPT::Bio::Lipo;
+use Moose;
+use strict;
+use warnings;
+use Data::Dumper;
+use autodie;
+
+# ABSTRACT: Lipo finding functionality in a library.
+
+sub run_hash {
+	my ( $self, $hash_ref ) = @_;
+	my %hash = %{$hash_ref};
+	my @return_keys;
+	foreach ( sort { $a <=> $b } keys %hash ) {
+		if ( $hash{$_}[4] !~ qr/^.{10,39}C/ ) {
+			next;
+		}
+		else {
+			$hash{$_}[5] = $self->run_seq( $hash{$_}[4] );
+		}
+	}
+	return \%hash;
+}
+
+sub run_seq {
+	my ( $self, $seq ) = @_;
+	my @C;    #A list of each C in the string, in str(10,40)
+	for ( my $j = 10 ; $j < length($seq) && $j < 40 ; $j++ ) {
+		if ( substr( $seq, $j, 1 ) =~ /[c]/i ) {
+			push( @C, $j );
+		}
+	}
+	my @results;
+	for ( my $z = 0 ; $z < scalar(@C) ; $z++ ) {
+		my $upC10 = "";
+
+      #Make sure it's not ALL DEKRs 10 residues upstream. (Does that happen O.o)
+		if ( substr( $seq, $C[$z] - 10, 10 ) !~ /[DEKR]/ ) {
+			push(
+				@results,
+				[
+					substr( $seq, 0, $C[$z] - 10 ),
+					substr( $seq, $C[$z] - 10, 10 ),
+					substr( $seq, $C[$z],      1 ),
+					substr( $seq, $C[$z] + 1 ),
+				]
+			);
+		}
+	}
+	if ( scalar @results ) {
+		return \@results;
+	}
+	return undef;
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Bio::Lipo - Lipo finding functionality in a library.
+
+=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