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revision 1.28, Wed Sep 16 09:34:32 2009 UTC revision 1.29, Tue Mar 16 16:01:54 2010 UTC
# Line 384  Line 384 
384      foreach my $peg ( @$pinned_pegs )      foreach my $peg ( @$pinned_pegs )
385      {      {
386          my $genome = $fig->genome_of($peg);          my $genome = $fig->genome_of($peg);
387          my $loc    = $fig->feature_location($peg);          my $loc;
388            if ($peg =~ /^fig\|\d+\.\d+\.(.+\_\d+\_\d+)$/) {
389                $loc = $1;
390            } else {
391                $loc = $fig->feature_location($peg);
392            }
393          # We only proceed if a location was found. Failure to find a location indicates          # We only proceed if a location was found. Failure to find a location indicates
394          # that the feature is deleted.          # that the feature is deleted.
395          if ($loc) {          if ($loc) {
# Line 872  Line 877 
877      if ($ENV{"PATH"} !~ /fig\/bin/) { $ENV{"PATH"} = "$FIG_Config::bin:" . $ENV{"PATH"}; }      if ($ENV{"PATH"} !~ /fig\/bin/) { $ENV{"PATH"} = "$FIG_Config::bin:" . $ENV{"PATH"}; }
878    
879      # Get amino acid sequences      # Get amino acid sequences
880      my @pegs = grep {$feature_data->{$_}{'type'} eq 'peg'} keys %$feature_data;      my @pegs = grep {$feature_data->{$_}{'type'} && $feature_data->{$_}{'type'} eq 'peg'} keys %$feature_data;
881      my $sequences = &get_peg_sequences($fig, \@pegs);      my $sequences = &get_peg_sequences($fig, \@pegs);
882    
883      # Write the entire set of sequences to a fasta file      # Write the entire set of sequences to a fasta file

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