lib/CXGN/Accession.pm

   1 use strict;
   2 use CXGN::DB::Connection;
   3 use CXGN::Tools::Text;
   4 use CXGN::DB::SQLWrappers;
   5 package CXGN::Accession;
   6
   7 =head1 NAME
   8
   9 CXGN::Accession
  10
  11 =head1 DESCRIPTION
  12
  13 Gets accession data from the sgn.accession and sgn.accession_names tables.
  14
  15 Note: will be soon deprecated in favor of the chado stock table.
  16
  17 =head1 AUTHOR
  18
  19 Takes an accession id or an accession name and returns a new accession object.
  20 With no accession id or name, it creates an empty accession object.
  21
  22 john binns - John Binns <zombieite@gmail.com>
  23
  24
  25 Code and POD style reformatting by Lukas.
  26
  27
  28 =head1 OBJECT METHODS
  29
  30 This class implements the following methods:
  31
  32 =cut
  33
  34
  35 =head2 new
  36
  37 Takes an accession id or an accession name and returns a new accession object. With no accession id or name, it creates an empty accession object.
  38
  39     use CXGN::Accession;
  40     my $accession=CXGN::Accession->new($dbh,$accession_name);
  41
  42 =cut
  43
  44 sub new {
  45     my $class=shift;
  46     my($dbh,$accession)=@_;
  47     unless(CXGN::DB::Connection::is_valid_dbh($dbh)){die"Invalid DBH.";}
  48     my $self=bless({},$class);
  49     $self->{dbh}=$dbh;
  50     if($accession) {
  51         my $id_query;
  52         if($accession=~/^\d+$/) {
  53             $id_query=$self->{dbh}->prepare('SELECT accession_id FROM accession WHERE accession_id=?');
  54         }
  55         else {
  56             $accession = '%'.$accession.'%';
  57             $id_query=$self->{dbh}->prepare('SELECT accession_id FROM accession_names WHERE accession_name ilike ?');
  58         }
  59         $id_query->execute($accession);
  60         ($self->{accession_id})=$id_query->fetchrow_array();
  61         if($self->{accession_id}) {
  62             my $accession_query=$self->{dbh}->prepare('SELECT organism.organism_id,organism_name,common_name.common_name_id,
  63                                           common_name.common_name,accession.common_name, accession.accession_name_id,
  64                                           accession_names.accession_name, accession.chado_organism_id
  65                                           FROM accession
  66                                           LEFT JOIN accession_names USING (accession_name_id)
  67                                           LEFT JOIN organism ON (accession.organism_id=organism.organism_id)
  68                                           LEFT JOIN common_name USING (common_name_id)
  69                                           WHERE accession.accession_id=?'
  70                                         );
  71
  72             $accession_query->execute($self->{accession_id});
  73             ($self->{organism_id},
  74              $self->{organism_name},
  75              $self->{organism_common_name_id},
  76              $self->{organism_common_name},
  77              $self->{accession_common_name},
  78              $self->{preferred_name_id},
  79              $self->{preferred_name},
  80              $self->{chado_organism_id})=$accession_query->fetchrow_array();
  81             my @aliases;
  82             my $aliases_query=$self->{dbh}->prepare('SELECT accession_name
  83                                                        FROM accession_names
  84                                                        WHERE accession_id=? AND  accession_name!=?'
  85                                                    );
  86             $aliases_query->execute($self->{accession_id},$self->{preferred_name});
  87             while(my($alias)=$aliases_query->fetchrow_array)
  88             {
  89                 push(@aliases,$alias);
  90             }
  91             $self->{aliases}=\@aliases;
  92         }
  93         else {
  94             return undef;
  95         }
  96     }
  97     return $self;
  98 }
  99
 100 =head2 all_accessions
 101
 102  Usage:        my %hash = CXGN::Accession->all_accessions($dbh);
 103  Desc:         class method that returns all the accessions
 104                as a hash of class_ids and accession names.
 105  Author:       added by Lukas 10/2009
 106
 107 =cut
 108
 109 sub all_accessions {
 110     my $class = shift;
 111     my $dbh = shift;
 112
 113     my $q = "SELECT accession_id, organism_name, accession_name FROM sgn.accession join sgn.accession_names using(accession_id) join sgn.organism using(organism_id)";
 114     my $h = $dbh->prepare($q);
 115     $h->execute();
 116     my %hash = ();
 117     while (my ($accession_id, $organism_name, $accession_name) = $h->fetchrow_array()) {
 118         $hash{$accession_id} = "$organism_name ($accession_name)";
 119     }
 120
 121     return %hash;
 122
 123 }
 124
 125 =head2 accession_id
 126
 127     my $id=$accession->accession_id();
 128
 129 =cut
 130
 131 sub accession_id {
 132     my $self=shift;
 133     return $self->{accession_id};
 134 }
 135
 136 =head2 preferred_name
 137
 138     my $accession_name=$accession->preferred_name();
 139
 140 =cut
 141
 142 sub preferred_name {
 143     my $self=shift;
 144     if(@_)
 145     {
 146         ($self->{preferred_name})=@_;
 147     }
 148     return $self->{preferred_name};
 149 }
 150
 151 =head2 other_names
 152
 153     my @aliases=@{$accession->other_names()};
 154
 155 =cut
 156
 157 sub other_names {
 158     my $self=shift;
 159     return @{$self->{aliases}};
 160 }
 161
 162 =head2 accession_common_name
 163
 164     my $acn=$accession->accession_common_name();
 165
 166 =cut
 167
 168 sub accession_common_name {
 169     my $self=shift;
 170     if(@_) {
 171         ($self->{accession_common_name})=@_;
 172     }
 173     return $self->{accession_common_name};
 174 }
 175
 176 =head2 chado_organism_id
 177
 178     my $acn=$accession->chado_organism_id();
 179
 180 =cut
 181
 182 sub chado_organism_id {
 183     my $self=shift;
 184     if(@_) {
 185         ($self->{chado_organism_id})=@_;
 186     }
 187     return $self->{chado_organism_id};
 188 }
 189
 190 =head2 organism_name
 191
 192     my $org_name=$accession->organism_name();
 193
 194 =cut
 195
 196 sub organism_name {
 197     my $self=shift;
 198     if(@_)
 199     {
 200         ($self->{organism_name})=@_;
 201     }
 202     return $self->{organism_name};
 203 }
 204
 205 =head2 organism_common_name
 206
 207     my $org_cn=$accession->organism_common_name();
 208
 209 =cut
 210
 211 sub organism_common_name {
 212     my $self=shift;
 213     if(@_)
 214     {
 215         ($self->{organism_common_name})=@_;
 216     }
 217     return $self->{organism_common_name};
 218 }
 219
 220 =head2 verbose_name
 221
 222     my $verbose_name = $accession->verbose_name();
 223
 224 =cut
 225
 226 sub verbose_name {
 227     my $self=shift;
 228     my $verbose_name=$self->{organism_name}." ".$self->{preferred_name};
 229     $verbose_name=CXGN::Tools::Text::abbr_latin($verbose_name);
 230     $verbose_name=~s/ \(.*\)//;
 231     return $verbose_name;
 232 }
 233
 234 =head2 extra_verbose_name
 235
 236     my $xvn=$accession->extra_verbose_name();
 237
 238 =cut
 239
 240 sub extra_verbose_name {
 241     my $self=shift;
 242     my @extra_verbose_name;
 243     if($self->{organism_common_name}) {
 244         push(@extra_verbose_name,"<b>".$self->{organism_common_name}."</b>");
 245     }
 246     if($self->{organism_name}) {
 247         push(@extra_verbose_name,$self->{organism_name});
 248     }
 249 #     if($self->{accession_common_name})
 250 #     {
 251 #         push(@extra_verbose_name,$self->{accession_common_name});
 252 #     }
 253     if($self->{preferred_name}) {
 254         push(@extra_verbose_name,$self->{preferred_name});
 255     }
 256     if(@{$self->{aliases}}[0]) {
 257         push(@extra_verbose_name,'('.join(', ',@{$self->{aliases}}).')');
 258     }
 259     my $extra_verbose_name=join(' ',@extra_verbose_name);
 260     $extra_verbose_name=CXGN::Tools::Text::abbr_latin($extra_verbose_name);
 261     return $extra_verbose_name;
 262 }
 263
 264 1;