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revision 1.13, Sat Feb 26 19:05:31 2011 UTC revision 1.14, Wed Jun 15 20:04:50 2011 UTC
# Line 29  Line 29 
29      use LoaderUtils;      use LoaderUtils;
30      use Digest::MD5;      use Digest::MD5;
31      use SeedUtils;      use SeedUtils;
32        use gjoseqlib;
33      use base 'BaseSaplingLoader';      use base 'BaseSaplingLoader';
34    
35  =head1 Sapling Feature Load Group Class  =head1 Sapling Feature Load Group Class
# Line 201  Line 202 
202          $self->Add(missingAliasFile => 1);          $self->Add(missingAliasFile => 1);
203          $aliasHash = {};          $aliasHash = {};
204      }      }
205        # Get all of this genome's protein sequences.
206        my %seqs = map { $_->[0] => $_->[2] } gjoseqlib::read_fasta("$FIG_Config::organisms/$genomeID/Features/peg/fasta");
207      # Get all of this genome's features.      # Get all of this genome's features.
208      my $featureList = $fig->all_features_detailed_fast($genomeID);      my $featureList = $fig->all_features_detailed_fast($genomeID);
209      # Loop through them.      # Loop through them.
# Line 324  Line 327 
327          my $proteinID;          my $proteinID;
328          if ($type eq 'peg') {          if ($type eq 'peg') {
329              # Get the translation.              # Get the translation.
330              my $proteinSequence = $fig->get_translation($fid);              my $proteinSequence = $seqs{$fid};
331              if (! $proteinSequence) {              if (! $proteinSequence) {
332                  Trace("No protein sequence found for $fid.") if T(ERDBLoadGroup => 2);                  Trace("No protein sequence found for $fid.") if T(ERDBLoadGroup => 2);
333                  $self->Add(missingProtein => 1);                  $self->Add(missingProtein => 1);

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