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annotate lib/CPT/Bio/DataSource/Chado.pm @ 1:d724f34e671d draft default tip

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author cpt
date Mon, 05 Jun 2023 02:50:07 +0000
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1 package CPT::Bio::DataSource::Chado;
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2 no warnings;
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3 use Moose;
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4 with 'CPT::Bio::DataSource';
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5
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6 has 'host' => ( is => 'rw', isa => 'Str' );
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7 has 'pass' => ( is => 'rw', isa => 'Str' );
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8 has 'user' => ( is => 'rw', isa => 'Str' );
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9 has 'name' => ( is => 'rw', isa => 'Str' );
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10 has 'port' => ( is => 'rw', isa => 'Str' );
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11
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12 has 'landmark' => ( is => 'rw', isa => 'Str' );
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13 has 'organism' => ( is => 'rw', isa => 'Str' );
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14
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15
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16 sub getSeqIO {
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17 my ($self) = @_;
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18 require CPT::Chado::GMOD_Conf;
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19
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20 my $db = Bio::DB::Das::Chado->new(
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21 -dsn => sprintf( 'dbi:Pg:dbname=%s;host=%s;port=%s', $self->name(), $self->host(), $self->port() ),
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22 -user => $self->user(),
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23 -pass => $self->pass(),
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24 -organism => $self->organism(),
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25 -inferCDS => 1,
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26
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27 );
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28
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29 # Get a list of "segments". Essentially (seqlen IS NOT NULL)
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30 my @segments = $db->segment( -name => $self->{'landmark'} );
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31
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32 # TODO: Need to have a fallback method
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33 # Should only produce ONE since we specify landmark exactly
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34 foreach my $segment (@segments) {
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35 my $stream = $segment->get_feature_stream();
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36 use Bio::Seq;
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37 my $seq_obj = Bio::Seq->new(
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38 -seq => $segment->seq->seq(),
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39 -display_id => $segment->id()
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40 );
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41 use Bio::SeqFeature::Generic;
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42 while ( my $feat = $stream->next_seq ) {
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43
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44 # In an IDEAL world we'd just do $seq_obj->add_SeqFeature($feat);
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45 #
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46 # HOWEVER.
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47 #
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48 # ------------- EXCEPTION: Bio::Root::NotImplemented -------------
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49 # MSG: Abstract method "Bio::DB::Das::Chado::Segment::Feature::attach_seq" is not implemented by package Bio::DB::Das::Chado::Segment::Feature.
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50 # This is not your fault - author of Bio::DB::Das::Chado::Segment::Feature should be blamed!
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51 # STACK: Error::throw
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52 # STACK: Bio::Root::Root::throw /usr/local/share/perl/5.14.2/Bio/Root/Root.pm:472
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53 # STACK: Bio::Root::RootI::throw_not_implemented /usr/local/share/perl/5.14.2/Bio/Root/RootI.pm:748
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54 # STACK: Bio::DB::Das::Chado::Segment::Feature::attach_seq /usr/local/share/perl/5.14.2/Bio/DB/Das/Chado/Segment/Feature.pm:374
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55 # STACK: Bio::Seq::add_SeqFeature /usr/local/share/perl/5.14.2/Bio/Seq.pm:1148
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56 # STACK: chado_export.pl:59
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57 # ----------------------------------------------------------------
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58
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59 # BUT WE CAN'T. >_> rageface.tiff
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60
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61 my %keys;
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62 foreach my $tag ( $feat->get_all_tags() ) {
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63 my @values = $feat->get_tag_values($tag);
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64 if ( $tag eq 'Note' ) {
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65 $tag = 'note';
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66 }
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67 if ( $tag eq 'Dbxref' ) {
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68 $tag = 'db_xref';
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69
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70 #@values = map { if($_ ne 'GFF_source:Genbank'){ $_ } } @values;
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71 @values = grep !/GFF_source:Genbank/, @values;
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72 }
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73 $keys{$tag} = \@values;
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74 }
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75
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76 #print $feat->gff_string(),"\n";
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77 my $new_feat = new Bio::SeqFeature::Generic(
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78 -start => $feat->start(),
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79 -end => $feat->end(),
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80 -strand => $feat->strand(),
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81 -primary_tag => $feat->primary_tag(),
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82 -tag => \%keys,
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83 );
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84 $seq_obj->add_SeqFeature($new_feat);
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85 }
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86
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87 return $seq_obj;
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88 }
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89
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90 }
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91
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92 no Moose;
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93 1;
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94
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95 __END__
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96
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97 =pod
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98
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99 =encoding UTF-8
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100
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101 =head1 NAME
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102
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103 CPT::Bio::DataSource::Chado
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104
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105 =head1 VERSION
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106
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107 version 1.99.4
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108
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109 =head2 getSeqIO
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110
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111 supposed to get a seqIO object from a chado DB. not fully implemented
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112
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113 =head1 AUTHOR
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114
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115 Eric Rasche <rasche.eric@yandex.ru>
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116
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117 =head1 COPYRIGHT AND LICENSE
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118
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119 This software is Copyright (c) 2014 by Eric Rasche.
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120
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121 This is free software, licensed under:
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122
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123 The GNU General Public License, Version 3, June 2007
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124
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125 =cut