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Diff of /Sprout/FeatureSaplingLoader.pm

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revision 1.12, Sun Feb 13 13:02:30 2011 UTC revision 1.13, Sat Feb 26 19:05:31 2011 UTC
# Line 326  Line 326 
326              # Get the translation.              # Get the translation.
327              my $proteinSequence = $fig->get_translation($fid);              my $proteinSequence = $fig->get_translation($fid);
328              if (! $proteinSequence) {              if (! $proteinSequence) {
329                  Trace("No protein sequence found for $fid.") if T(2);                  Trace("No protein sequence found for $fid.") if T(ERDBLoadGroup => 2);
330                  $self->Add(missingProtein => 1);                  $self->Add(missingProtein => 1);
331                  # Here there was some sort of error and the protein sequence did                  # Here there was some sort of error and the protein sequence did
332                  # not come back. Ask for the DNA and translate it instead.                  # not come back. Ask for the DNA and translate it instead.
# Line 351  Line 351 
351          for my $aliasTuple (@$aliasList) {          for my $aliasTuple (@$aliasList) {
352              my ($aliasID, $aliasType, $aliasConf) = @$aliasTuple;              my ($aliasID, $aliasType, $aliasConf) = @$aliasTuple;
353              # Get the natural form. If there is none, then the canonical              # Get the natural form. If there is none, then the canonical
354              # form IS the natural form.              # form IS the natural form. Note we have to make a special check
355              my $natural = AliasAnalysis::Type($aliasType => $aliasID) || $aliasID;              # for locus tags, which have an insane number of variants.
356                my $natural;
357                if ($aliasID =~ /LocusTag:(.+)/) {
358                    $natural = $1;
359                } else {
360                    $natural = AliasAnalysis::Type($aliasType => $aliasID) || $aliasID;
361                }
362              # Create the identifier record.              # Create the identifier record.
363              $self->PutE(Identifier => $aliasID, natural_form => $natural,              $self->PutE(Identifier => $aliasID, natural_form => $natural,
364                          source => $aliasType);                          source => $aliasType);

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