Add evaluation and embedding code

.gitignore

ContextEmbedding/binding_affinities_for_embedded_peptide.py

ContextEmbedding/create_embedded_input_peptides.py

ContextEmbedding/embedded_epitope_features.py

ContextEmbedding/reformat_netchop_out.py

ContextEmbedding/sars_netchop_to_pkl.py

Evaluation/binarize_entries.py

Evaluation/calculate_cleaved_peptides.py

Evaluation/calculate_protein_cleaved_peptides.py

Evaluation/compare_pep_count_vs_score.py

Evaluation/compare_single_vs_combined.py

Evaluation/compare_size_to_coverage.py

Evaluation/comparison_data.py

Evaluation/create_haplotype_ba_predictions.py

Evaluation/evaluate_cleavage_predictions.py

Evaluation/evaluate_vaccine.py

Evaluation/get_gifford_vax_length.py

Evaluation/plot_cleavage_predictions.py

Evaluation/plot_evaluation_results.py

Evaluation/read_peptides.py