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1 : parrello 1.1 #!/usr/bin/perl -w
2 :    
3 :     #
4 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
5 :     # for Interpretations of Genomes. All Rights Reserved.
6 :     #
7 :     # This file is part of the SEED Toolkit.
8 :     #
9 :     # The SEED Toolkit is free software. You can redistribute
10 :     # it and/or modify it under the terms of the SEED Toolkit
11 :     # Public License.
12 :     #
13 :     # You should have received a copy of the SEED Toolkit Public License
14 :     # along with this program; if not write to the University of Chicago
15 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
16 :     # Genomes at veronika@thefig.info or download a copy from
17 :     # http://www.theseed.org/LICENSE.TXT.
18 :     #
19 :    
20 :     package SynonymSproutLoader;
21 :    
22 :     use strict;
23 :     use Tracer;
24 :     use ERDB;
25 :     use base 'BaseSproutLoader';
26 :    
27 :     =head1 Sprout Synonym Load Group Class
28 :    
29 :     =head2 Introduction
30 :    
31 :     The Synonym Load Group includes all of the major non-redundancy tables.
32 :    
33 :     =head3 new
34 :    
35 :     my $sl = SynonymSproutLoader->new($erdb, $source, $options, @tables);
36 :    
37 :     Construct a new SynonymSproutLoader object.
38 :    
39 :     =over 4
40 :    
41 :     =item erdb
42 :    
43 :     [[SproutPm]] object for the database being loaded.
44 :    
45 :     =item source
46 :    
47 :     [[FigPm]] object used to access the source data. If this parameter is undefined,
48 :     it will be created the first time the L</source> method is called.
49 :    
50 :     =item options
51 :    
52 :     Reference to a hash of command-line options.
53 :    
54 :     =item tables
55 :    
56 :     List of tables in this load group.
57 :    
58 :     =back
59 :    
60 :     =cut
61 :    
62 :     sub new {
63 :     # Get the parameters.
64 :     my ($class, $erdb, $source, $options) = @_;
65 :     # Create the table list.
66 :     my @tables = sort qw(SynonymGroup SynonymGroupFor);
67 :     # Create the BaseSproutLoader object.
68 :     my $retVal = BaseSproutLoader::new($class, $erdb, $source, $options, @tables);
69 :     # Return it.
70 :     return $retVal;
71 :     }
72 :    
73 :     =head2 Public Methods
74 :    
75 :     =head3 Generate
76 :    
77 :     $sl->Generate();
78 :    
79 :     Generate the data for the non-redundancy files.
80 :    
81 :     =cut
82 :    
83 :     sub Generate {
84 :     # Get the parameters.
85 :     my ($self) = @_;
86 :     # Get the sprout object.
87 :     my $sprout = $self->db();
88 :     # Get the FIG object.
89 :     my $fig = $self->source();
90 :     # Is this the global section?
91 :     if (! $self->global()) {
92 :     # No, then get the section ID.
93 :     my $genomeID = $self->section();
94 :     # Get the database handle.
95 :     my $dbh = $fig->db_handle();
96 :     # Ask for the synonyms. Note that "maps_to" is a group name, and "syn_id" is a PEG ID or alias.
97 :     my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms WHERE syn_id LIKE ?");
98 :     my $result = $sth->execute("FIG|$genomeID%");
99 :     if (! defined($result)) {
100 :     Confess("Database error in Synonym load: " . $sth->errstr());
101 :     } else {
102 :     Trace("Processing synonym results for $genomeID.") if T(2);
103 :     # Loop through the synonym/peg pairs.
104 :     while (my @row = $sth->fetchrow()) {
105 :     # Get the synonym group ID and feature ID.
106 :     my ($syn_id, $peg) = @row;
107 :     # Count this row.
108 :     $self->Add('synonyms-read' => 1);
109 :     # Insure it's not deleted.
110 :     if ($fig->is_deleted_fig($peg)) {
111 :     $self->Add('synonyms-skipped' => 1);
112 :     } else {
113 :     # Create the group record.
114 :     $self->PutE(SynonymGroup => $syn_id);
115 :     # Connect the synonym to the peg.
116 :     $self->PutR(SynonymGroup => $syn_id, $peg);
117 :     }
118 :     }
119 :     }
120 :     }
121 :     }
122 :    
123 :    
124 :     1;

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