lib/CXGN/Bulk/Converter.pm

   1
   2 use strict;
   3
   4 package CXGN::Bulk::Converter;
   5
   6 use base 'CXGN::Bulk';
   7 use File::Slurp;
   8
   9 our %solyc_conversion_hash;
  10
  11 sub process_parameters {
  12     my $self = shift;
  13     $self->{output_fields} = [ 'Input', 'Output' ];
  14
  15     my @ids = split /\s+/, $self->{ids};
  16
  17     $self->{ids} = \@ids;
  18
  19     if (@ids) {
  20         return 1;
  21     }
  22     else {
  23         return 0;
  24     }
  25 }
  26
  27 sub process_ids {
  28     my $self = shift;
  29
  30     if (!%solyc_conversion_hash) {
  31         $self->get_hash();
  32     }
  33
  34     $self->{query_start_time} = time();
  35     my ($dump_fh, $notfound_fh) = $self->create_dumpfile();
  36     my @not_found = ();
  37     foreach my $id (@{$self->{ids}}) {
  38         print STDERR "Converting $id to $solyc_conversion_hash{uc($id)}\n";
  39         if (exists($solyc_conversion_hash{uc($id)})) {
  40             print $dump_fh "$id\t$solyc_conversion_hash{uc($id)}\n";
  41         }
  42         else {
  43             print $notfound_fh "$id\t(not found)\n";
  44         }
  45     }
  46     close($dump_fh);
  47     close($notfound_fh);
  48     $self->{query_time} = time() - $self -> {query_start_time};
  49 }
  50
  51 sub get_hash {
  52     my $self = shift;
  53
  54     print STDERR "Generating hash... ";
  55
  56     my @conversion = ();
  57     foreach my $file (@{$self->{solyc_conversion_files}}) {
  58         print STDERR "(processing $file) ";
  59         my @lines = read_file($file);
  60         @conversion = (@conversion, @lines);
  61     }
  62
  63     foreach my $entry (@conversion) {
  64         my @fields = split /\t/, $entry;
  65         $solyc_conversion_hash{uc($fields[0])} = $fields[1];
  66     }
  67
  68     print STDERR "Done.\n";
  69
  70 }
  71
  72 1;