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annotate lib/CPT/Bio/Lipo.pm @ 1:f093e08f21f3 draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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1 package CPT::Bio::Lipo;
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2 use Moose;
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3 use strict;
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4 use warnings;
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5 use Data::Dumper;
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6 use autodie;
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7
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8 # ABSTRACT: Lipo finding functionality in a library.
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9
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10 sub run_hash {
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11 my ( $self, $hash_ref ) = @_;
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12 my %hash = %{$hash_ref};
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13 my @return_keys;
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14 foreach ( sort { $a <=> $b } keys %hash ) {
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15 if ( $hash{$_}[4] !~ qr/^.{10,39}C/ ) {
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16 next;
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17 }
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18 else {
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19 $hash{$_}[5] = $self->run_seq( $hash{$_}[4] );
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20 }
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21 }
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22 return \%hash;
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23 }
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24
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25 sub run_seq {
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26 my ( $self, $seq ) = @_;
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27 my @C; #A list of each C in the string, in str(10,40)
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28 for ( my $j = 10 ; $j < length($seq) && $j < 40 ; $j++ ) {
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29 if ( substr( $seq, $j, 1 ) =~ /[c]/i ) {
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30 push( @C, $j );
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31 }
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32 }
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33 my @results;
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34 for ( my $z = 0 ; $z < scalar(@C) ; $z++ ) {
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35 my $upC10 = "";
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36
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37 #Make sure it's not ALL DEKRs 10 residues upstream. (Does that happen O.o)
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38 if ( substr( $seq, $C[$z] - 10, 10 ) !~ /[DEKR]/ ) {
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39 push(
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40 @results,
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41 [
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42 substr( $seq, 0, $C[$z] - 10 ),
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43 substr( $seq, $C[$z] - 10, 10 ),
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44 substr( $seq, $C[$z], 1 ),
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45 substr( $seq, $C[$z] + 1 ),
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46 ]
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47 );
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48 }
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49 }
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50 if ( scalar @results ) {
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51 return \@results;
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52 }
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53 return undef;
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54 }
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55
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56 no Moose;
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57 1;
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58
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59 __END__
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60
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61 =pod
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62
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63 =encoding UTF-8
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64
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65 =head1 NAME
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66
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67 CPT::Bio::Lipo - Lipo finding functionality in a library.
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68
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69 =head1 VERSION
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70
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71 version 1.99.4
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72
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73 =head1 AUTHOR
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74
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75 Eric Rasche <rasche.eric@yandex.ru>
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76
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77 =head1 COPYRIGHT AND LICENSE
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78
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79 This software is Copyright (c) 2014 by Eric Rasche.
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80
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81 This is free software, licensed under:
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82
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83 The GNU General Public License, Version 3, June 2007
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84
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85 =cut