lib/CXGN/Tools/Organism.pm

   1
   2
   3
   4 =head1 NAME
   5
   6 Functions for accessing ogranism names and their identifiers
   7
   8 =head1 SYNOPSIS
   9
  10
  11 =head1 DESCRIPTION
  12
  13
  14 =cut
  15
  16
  17 =head2 get_all_organisms
  18
  19  Usage:        my ($names_ref, $ids_ref) = CXGN::Tools::Organism::get_all_organisms($dbh, %return_hash_flag);
  20  Desc:         This is a static function. Retrieves distinct organism names and IDs from sgn.common_name
  21  Ret:          Returns two arrayrefs. One array contains all the
  22                organism names, and the other all the organism ids
  23                with corresponding array indices
  24                or a hash {common_name}=common_name_id if 2nd argument is provided
  25
  26  Args:         a database handle, a boolean (optional)
  27  Side Effects:
  28  Example:
  29
  30 =cut
  31
  32 package CXGN::Tools::Organism;
  33
  34 use strict;
  35 use warnings;
  36
  37
  38
  39
  40 sub get_all_organisms {
  41     my $dbh = shift;
  42     my $return_hash = shift;
  43     #this query should be changed to work with chado's organism table after sgn.common_name is replaced with it.
  44     my $query = "SELECT common_name, common_name_id
  45                    FROM sgn.common_name ORDER BY upper(common_name) desc";
  46     my $sth = $dbh->prepare($query);
  47     $sth->execute();
  48     my @names = ();
  49     my @ids = ();
  50      my %common_names=();
  51     while (my($common_name, $common_name_id) = $sth->fetchrow_array()) {
  52         push @names, $common_name;
  53         push @ids, $common_name_id;
  54         $common_names{$common_name}= $common_name_id;
  55     }
  56     return %common_names if $return_hash;
  57     return (\@names, \@ids);
  58 }
  59
  60
  61 =head2 get_existing_organisms
  62
  63  Usage:        my ($names_ref, $ids_ref) = CXGN::Tools::Organism::get_existing_organisms($dbh , return_hash_flag);
  64  Desc:         This is a static function. Selects the distinct organism names and their IDs from phenome.locus.
  65                Useful for populating a unique drop-down menu with only the organism names that exist in the table.
  66  Ret:          Returns two arrayrefs. One array contains all the
  67                organism names, and the other all the organism ids with corresponding array indices.
  68               or a hash {common_name}=common_name_id if 2nd argument is provided
  69  Args:         a database handle, and a boolean (optional)
  70  Side Effects:
  71  Example:
  72
  73 =cut
  74
  75 sub get_existing_organisms {
  76     my $dbh= shift;
  77     my $return_hash = shift;
  78     my $query = "SELECT distinct(common_name), common_name_id FROM phenome.locus
  79                  JOIN sgn.common_name using(common_name_id)
  80                  WHERE obsolete = 'f'";
  81     my $sth = $dbh->prepare($query);
  82     $sth->execute();
  83     my @names = ();
  84     my @ids = ();
  85     my %common_names=();
  86     while (my($common_name, $common_name_id) = $sth->fetchrow_array()) {
  87         push @names, $common_name;
  88         push @ids, $common_name_id;
  89         $common_names{$common_name}= $common_name_id;
  90     }
  91     return %common_names if $return_hash;
  92     return (\@names, \@ids);
  93 }
  94
  95 =head2 get_all_populations
  96
  97  Usage:        my ($names_ref, $ids_ref) = CXGN::Tools::Organism::get_all_populations($dbh);
  98  Desc:         This is a static function. Retrieves distinct population names and IDs from phenome.population
  99  Ret:          Returns two arrayrefs. One array contains all the
 100                population names, and the other all the population ids
 101                with corresponding array indices.
 102  Args:         a database handle
 103  Side Effects:
 104  Example:
 105
 106 =cut
 107
 108 sub get_all_populations {
 109     my $dbh = shift;
 110
 111     my $query = "SELECT name, population_id
 112                    FROM phenome.population";
 113     my $sth = $dbh->prepare($query);
 114     $sth->execute();
 115     my @names = ();
 116     my @ids = ();
 117     while (my($name, $population_id) = $sth->fetchrow_array()) {
 118         push @names, $name;
 119         push @ids, $population_id;
 120     }
 121     return (\@names, \@ids);
 122 }
 123
 124
 125 =head2 organism_id_specie
 126
 127  Usage: $id = CXGN::Tools::Organism::organism_id_specie($dbh, $specie);
 128  Desc: retrieves the organism id from sgn.organism
 129  Ret: organism id
 130  Args: db handle, specie name (eg. solanum lycopersicum)
 131  Side Effects: access db
 132  Example:
 133
 134 =cut
 135
 136 sub organism_id_specie {
 137     my $dbh = shift;
 138     my $specie = shift;
 139
 140     print STDERR "specie_tax: $specie\n";
 141
 142     my $sth = $dbh->prepare("SELECT organism_id
 143                                     FROM sgn.organism
 144                                     WHERE specie_tax ILIKE ?"
 145                            );
 146     $sth->execute($specie);
 147     my $id;
 148     while (my $id_1 = $sth->fetchrow_array()) {
 149         $id = $id_1;
 150     }
 151     return $id;
 152
 153 }
 154
 155
 156
 157
 158 return 1;