A few further points to note:-

• Use the three-argument form of open with lexical file handles and check for success, giving the o/s error on failure, e.g.

  open my $uniqueFH, '<', $uniqueFile
     or die "open: < $uniqueFile: $!\n";
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• You can do your chomping in one fell swoop

  chomp( my @data_in = <$uniqueFH> );
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  rather than piecemeal.

• You could consider using a hash slice rather than looping although this might not be practicable with very large data sets

  my %strSpec_protein_hash;
  @strSpec_protein_hash{ @data_in } =
     @goodProteins_hash{ @data_in };
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• I wonder if you have a cut'n'paste error in your post, my %strSpec; versus $strSpec_protein_hash{$id} = $seq;

I hope these points are helpful.