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annotate lib/CPT/Bio/Dbxref.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::Dbxref;
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2 use Moose;
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3 use autodie;
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4 use YAML;
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5 use File::ShareDir;
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6 use File::Spec qw/catfile/;
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7
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8 has 'regex_map' => ( is => 'rw', isa => 'HashRef');
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9 has 'initialized' => ( is => 'rw', isa => 'Int', default => 0);
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10
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11 sub init {
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12 my ($self) = @_;
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13 # Locate file
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14 my $data_dir = File::ShareDir::dist_dir('libCPT');
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15 my $dbxref_data = File::Spec->catfile($data_dir, 'dbxref.yaml');
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16 # Parse
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17 $self->regex_map(YAML::LoadFile($dbxref_data));
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18 $self->initialized(1);
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19 }
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20
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21 sub get_prefix {
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22 my ($self, $dbxref) = @_;
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23 if(!$self->initialized()){
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24 $self->init();
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25 }
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26
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27 my @hits;
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28 my %map = %{$self->regex_map()};
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29 # Search through regex database
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30 foreach my $db(keys(%map)){
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31 if(defined($map{$db}{local_id_syntax})){
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32 my $ref = $map{$db}{local_id_syntax};
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33 if(ref($ref) eq 'ARRAY'){
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34 foreach my $regi(@{$ref}){
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35 if($dbxref =~ /$regi/){
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36 push(@hits, $map{$db}{abbreviation});
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37 }
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38 }
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39 }
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40 if($dbxref =~ /$ref/){
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41 push(@hits, $map{$db}{abbreviation});
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42 }
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43 }
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44 }
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45 return @hits;
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46 }
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47
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48
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49 no Moose;
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50 1;
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51
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52 __END__
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53
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54 =pod
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55
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56 =encoding UTF-8
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57
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58 =head1 NAME
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59
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60 CPT::Bio::Dbxref
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61
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62 =head1 VERSION
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63
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64 version 1.99.4
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65
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66 =head1 AUTHOR
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67
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68 Eric Rasche <rasche.eric@yandex.ru>
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69
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70 =head1 COPYRIGHT AND LICENSE
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71
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72 This software is Copyright (c) 2014 by Eric Rasche.
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73
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74 This is free software, licensed under:
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75
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76 The GNU General Public License, Version 3, June 2007
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77
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78 =cut