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author | cpt |
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date | Mon, 05 Jun 2023 02:47:24 +0000 |
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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