arriba output containing ? in peptide sequence will trigger error in manufacturability calculations

Installation Type

Standalone

pVACtools Version / Docker Image

4.0.1

Python Version

3.8

Operating System

No response

Describe the bug

Arriba outputs are allowed to contain ? in the peptide_sequence and fusion_transcript columns. This will trigger an error in the manufacturability calculations as ? is not an amino acid in the dict. See the error message in log output below.

How to reproduce this bug

I've provided an example, I modified a bit the content, but the issues are the same. `?` containing sequences will trigger an error.

Input files

#gene1  gene2   strand1(gene/fusion)    strand2(gene/fusion)    breakpoint1 breakpoint2 site1   site2   type    split_reads1    split_reads2    discordant_mates    coverage1   coverage2   confidence  reading_frame   tags    retained_protein_domains    closest_genomic_breakpoint1 closest_genomic_breakpoint2 gene_id1    gene_id2    transcript_id1  transcript_id2  direction1  direction2  filters fusion_transcript   peptide_sequence    read_identifiers
PTEN    ENSG00000200891(21548),MED6P1(31892)    +/+ ./+ chr10:87952259  chr10:88016243  CDS/splice-site intergenic  deletion/read-through   163 146 6   3691    3002    high    out-of-frame    .   C2_domain_of_PTEN_tumour-suppressor_protein(100%),Dual_specificity_phosphatase__catalytic_domain(100%)| .   .   ENSG00000171862 .   ENST00000371953 .   downstream  upstream    duplicates(384),low_entropy(4),mismappers(15),mismatches(6),multimappers(2) CCTCACCTCCATGCAGATGCAGCTGTACCTGCAGCAGCTGCAGAAGGTGCAGCCCCCTACGCCGCTACTCCCTTCCGTGAAGGTGCAGTCCCAGCCCCCcCCCCCCCccCCcCCCCCcCCCCcCCCC|CCC??CCCCC?CCCCCCCTGCCGCCCCCACCCCACCCCTCTGTGCAGCAGCAGCTGCAGCAGCAGCCGCCACCACCCCCACCACCCCAGCCCCAGCCTCCACCCCAGCAGCAGCATCAGCCCCCTCCACGGCCCGTGCACTTGCAGCCCATGCAGTTTTCCACCCA  LTSMQMQLYLQQLQKVQPPTPLLPSVKVQSQPPPPpPPPPpP|p?p?ppcrphptplcssscsssrhhphhpspslhpsssisplhgpctcspcsfpp  K00193:38:H3MYFBBXX:4:1101:18904:31572,K00193:38:H3MYFBBXX:4:1101:20386:3197

Log output

Calculating Manufacturability Metrics
Traceback (most recent call last):
  File "/Users/boyangzhao/anaconda/envs/bio38/bin/pvacfuse", line 8, in <module>
    sys.exit(main())
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/pvactools/tools/pvacfuse/main.py", line 108, in main
    args[0].func.main(args[1])
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/pvactools/tools/pvacfuse/run.py", line 212, in main
    (input_file, per_epitope_output_dir) = generate_fasta(args, output_dir, epitope_length)
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/pvactools/tools/pvacfuse/run.py", line 82, in generate_fasta
    pvactools.tools.pvacfuse.generate_protein_fasta.main(params, save_tsv_file=True, starfusion_file=args.starfusion_file)
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/pvactools/tools/pvacfuse/generate_protein_fasta.py", line 132, in main
    CalculateManufacturability(args.output_file, manufacturability_file, 'fasta').execute()
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/pvactools/lib/calculate_manufacturability.py", line 47, in execute
    scores = ManufacturabilityScores.from_amino_acids(sequence)
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/vaxrank/manufacturability.py", line 148, in from_amino_acids
    return cls(*[fn(amino_acids) for fn in scoring_functions])
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/vaxrank/manufacturability.py", line 148, in <listcomp>
    return cls(*[fn(amino_acids) for fn in scoring_functions])
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/vaxrank/manufacturability.py", line 73, in max_7mer_gravy_score
    return max_kmer_gravy_score(amino_acids, 7)
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/vaxrank/manufacturability.py", line 67, in max_kmer_gravy_score
    return max(
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/vaxrank/manufacturability.py", line 68, in <genexpr>
    gravy_score(amino_acids[i:i + k])
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/vaxrank/manufacturability.py", line 56, in gravy_score
    total = sum(
  File "/Users/boyangzhao/anaconda/envs/bio38/lib/python3.8/site-packages/vaxrank/manufacturability.py", line 57, in <genexpr>
    hydropathy_dict[amino_acid] for amino_acid in amino_acids)
KeyError: '?'

Output files