adding test to make sure imputation improves predictive accuracy on a small allele, added allow_unknown_amino_acids to from_hyperparameters

fixed neural network test, fixed length filtering of data loading, started on adding imputation to training script

 - Add default values and usage to argparse help messages
 - Require theano >=0.8.2 (was getting errors instantiating a model at 0.7.0)