lib/CXGN/Tools/Parse/SignalP.pm

   1 package CXGN::Tools::Parse::SignalP;
   2 use strict;
   3
   4 =head1 CXGN::Tools::Parse::SignalP
   5
   6  Parses output from SignalP V 3.0 in short format
   7
   8 =head1 Author
   9
  10  C. Carpita <csc32@cornell.edu>
  11
  12 =head1 Methods
  13
  14 =cut
  15
  16 =head2 new()
  17
  18  Args: (opt) raw output data
  19  Ret: Parser object
  20  Side: Calls parse() automatically if argument provided
  21
  22 =cut
  23
  24 sub new {
  25         my $class = shift;
  26         my $self = bless {}, $class;
  27         my $data = shift;
  28         if($data){
  29                 $self->{data} = $data;
  30                 $self->parse();
  31         }
  32         return $self;
  33 }
  34
  35 sub parse_file {
  36         my $self = shift;
  37         my $filename = shift;
  38         die "No file: $filename" unless (-f $filename);
  39         open(FH, $filename);
  40         $self->{data} .= $_ while <FH>;
  41         close FH;
  42         $self->parse();
  43 }
  44
  45 sub parse {
  46         my $self = shift;
  47         my $data = $self->{data};
  48         $self->{entries} = [];
  49         $self->{entry_by_id} = {};
  50         while(<$data>){
  51                 next if /^\s*#/;
  52                 my %h = ();
  53                 ($h{id}, $h{nn_cmax}, $h{nn_cpos}, $h{nn_cdec},
  54                  $h{nn_ymax}, $h{nn_ypos}, $h{nn_ydec},
  55                  $h{nn_smax}, $h{nn_spos}, $h{nn_sdec},
  56                  $h{nn_smean}, $h{nn_smeandec}, $h{nn_score}, $h{nn_decision},
  57                  $h{hmm_decision}, $h{hmm_cmax}, $h{hmm_cpos}, $h{hmm_cdec},
  58                  $h{hmm_sprob}, $h{hmm_sdec}
  59                  )
  60                  =
  61                  /^(\S+)\s+(\S+)\s+(\d+)\s+([NY])\s+(\S+)\s+(\d+)\s+([NY])\s+(\S+)\s+(\d+)\s+([NY])\s+(\S+)\s+([NY])\s+(\S+)\s+([NY])\s+\S+\s+([A-Z]+)\s+(\S+)\s+(\d+)\s+([NY])\s+(\S+)\s+([NY])/;
  62                 push(@{$self->{entries}}, \%h);
  63                 $self->{entry_by_id}->{$h{id}} = \%h;
  64         }
  65 }
  66
  67 sub getEntryById {
  68         my $self = shift;
  69         my $id = shift;
  70         return $self->{entry_by_id}->{$id};
  71 }
  72
  73 sub getEntryArray {
  74         my $self = shift;
  75         return @{$self->{entries}};
  76 }
  77
  78 1;