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annotate lib/CPT/Bio/RBS/Algo/Naive.pm @ 1:8691c1c61a8e draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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1 package CPT::Bio::RBS::Algo::Naive;
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2 use Moose;
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3 with 'CPT::Bio::RBS::Algo';
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4 use CPT::Bio::RBS_Object;
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5
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6 my @SDs = (
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7 'aggaggt',
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8 'ggaggt',
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9 'aggagg',
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10 'aggag',
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11 'gaggt',
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12 'ggagg',
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13 'aggt',
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14 'gggt',
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15 'gagg',
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16 'gggg',
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17 'agga',
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18 'ggag',
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19 'gga',
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20 'gag',
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21 'agg',
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22 'ggt',
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23 );
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24
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25 sub predict {
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26 my ( $self, %params ) = @_;
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27 my $upstream = $params{sequence};
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28 my $only_best = $params{return_best};
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29
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30 my $length = length($upstream);
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31
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32 my @results = ();
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33 foreach my $rbs ( @SDs ){
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34 while ($upstream =~ /$rbs/g) {
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35 # Position of regex match
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36 my $loc = $-[0];
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37 # Seq before RBS
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38 my $before = substr($upstream,0, $loc);
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39 # Seq after RBS
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40 my $after = substr($upstream, $loc + length($rbs));
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41 my $rbs_o = CPT::Bio::RBS_Object->new(
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42 upstream => sprintf('%s %s %s', $before , uc($rbs) , $after),
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43 score => $self->score_match($rbs, length($after)),
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44 rbs_seq => uc($rbs),
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45 separation => length($after),
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46 );
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47 push( @results, $rbs_o );
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48 }
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49 }
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50 @results = sort { $b->score() <=> $a->score() } @results;
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51 if (@results) {
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52 if($only_best){
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53 return ($results[0]);
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54 }else{
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55 return @results;
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56 }
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57 }
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58 else {
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59 return (
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60 CPT::Bio::RBS_Object->new(
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61 upstream =>$upstream,
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62 score => '-1',
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63 rbs_seq => 'None',
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64 separation => -1,
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65 )
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66 );
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67 }
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68 }
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69
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70 sub score_match {
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71 my ($self, $match, $dist) = @_;
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72 return length($match);
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73 }
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74
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75 1;
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76
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77 __END__
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78
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79 =pod
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80
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81 =encoding UTF-8
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82
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83 =head1 NAME
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84
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85 CPT::Bio::RBS::Algo::Naive
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86
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87 =head1 VERSION
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88
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89 version 1.99.4
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90
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91 =head1 AUTHOR
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92
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93 Eric Rasche <rasche.eric@yandex.ru>
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94
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95 =head1 COPYRIGHT AND LICENSE
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96
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97 This software is Copyright (c) 2014 by Eric Rasche.
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98
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99 This is free software, licensed under:
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100
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101 The GNU General Public License, Version 3, June 2007
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102
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103 =cut