Mercurial > repos > cpt > cpt_psm_comparison_table
diff lib/CPT/Bio/Lipo.pm @ 1:f093e08f21f3 draft default tip
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author | cpt |
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date | Mon, 05 Jun 2023 02:47:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/CPT/Bio/Lipo.pm Mon Jun 05 02:47:24 2023 +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