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

   1
   2 package CXGN::Blast::SeqQuery::Plugin::ProteinSequence;
   3
   4 use Moose;
   5
   6 use Bio::Seq;
   7
   8 sub name {
   9     return "protein sequence";
  10 }
  11
  12 sub type {
  13     return 'protein';
  14 }
  15
  16 sub example {
  17     return "VHYNLFKMNGFHHTEIWDRHESFECSSVGSEESHSLEGGEKLYHDPSTEGQKEAGPKSELTSGVKSLDRCLSNPRSLGEIPASYEISEYE
  18 HLIEQEMRWLKANYQIKLRELKDQHLGLPPKASKPPTGSSKRKKKTKNKNSCLETLLKSSDCGKTISSESNGLSCPISVSQRARKCEAIK
  19 GSPNVRDMVSSAKSFFTRTLLPNSLHRTTSLPVDAVDI";
  20 }
  21
  22 sub validate {
  23     my $self = shift;
  24     my $c = shift;
  25     my $input = shift;
  26
  27     eval {
  28         my $s = Bio::Seq->new(-seq => $input);
  29
  30         if ($s->seq() !~ /^[ACDEFGHIKLMNPQRSTVWYX\n\s\t]$/i) {
  31             $c->stash->{rest} = { error=> "Protein sequence contains illegal characters: ".($s->id)};
  32             return;
  33         }
  34     };
  35     if ($@) {
  36         $c->stash->{rest} = {error => "The sequence does not seem to be a legal protein sequence.", };
  37         return;
  38     }
  39
  40     return "OK";
  41 }
  42
  43 sub process {
  44     my $self = shift;
  45     my $c = shift;
  46     my $sequence = shift;
  47
  48     return ">Untitled Sequence\n$sequence\n";
  49 }
  50
  51 1;