lib/CXGN/Blast/SeqQuery/Plugin/TomatoGenomeIds.pm

   1
   2 package CXGN::Blast::SeqQuery::Plugin::TomatoGenomeIds;
   3
   4 use Moose;
   5
   6 sub name {
   7     return "tomato genome identifiers";
   8 }
   9
  10 sub type {
  11     return 'nucleotide';
  12 }
  13
  14 sub example {
  15     return "Solyc01g005370
  16 Solyc01g005590
  17 Solyc01g016780
  18 Solyc01g058740
  19 Solyc01g080500";
  20 }
  21
  22 sub validate {
  23     my $self = shift;
  24     my $c = shift;
  25     my $input = shift;
  26
  27     my @ids = split /\s+/, $input;
  28
  29     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  30     my $rna_id = $schema->resultset("Cv::Cvterm")->find( { name=>'mRNA' })->cvterm_id();
  31
  32     my @missing = ();
  33     foreach my $id (@ids) {
  34         print STDERR "Validating $id... ";
  35         my $rs = $schema->resultset("Sequence::Feature")->search( { type_id=>$rna_id, name => { ilike => "$id".'.%.1' } } );
  36         if ($rs->count() ==0) {
  37             print STDERR " not found.\n";
  38             push @missing, $id;
  39         }
  40         else { print STDERR "OK\n"; }
  41
  42     }
  43     if (@missing) {
  44         return "The folloing ids entered do not exist: ".(join ",", @missing);
  45     }
  46     else {
  47         return "OK";
  48     }
  49 }
  50
  51 sub process {
  52     my $self = shift;
  53     my $c = shift;
  54     my $input = shift;
  55
  56     my @ids = split /\s+/, $input;
  57
  58     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  59     my $rna_id = $schema->resultset("Cv::Cvterm")->find( { name=>'mRNA' })->cvterm_id();
  60     print STDERR "RNA: $rna_id\n";
  61     my @seqs = ();
  62     foreach my $id (@ids) {
  63         my $rs = $schema->resultset("Sequence::Feature")->search( { type_id=>$rna_id, name => { ilike => "$id".'.%.1' } } );
  64         if (my $row = $rs->next()) {
  65
  66             push @seqs, ">".$row->name."\n".$row->residues();
  67         }
  68         else {
  69                     die "ID $id does not exist!";
  70         }
  71     }
  72     my $sequence =  join "\n", @seqs;
  73     print STDERR "SEQUENCE = $sequence\n";
  74
  75     return $sequence;
  76
  77
  78 }
  79
  80 1;
  81