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Optional Downstream Analysis Tools

Generate Protein Fasta

/home/docs/checkouts/readthedocs.org/user_builds/pvactools/conda/latest/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
usage: pvacseq generate_protein_fasta [-h] [-d DOWNSTREAM_SEQUENCE_LENGTH]
                                      input_file peptide_sequence_length
                                      output_file

positional arguments:
  input_file            A VEP-annotated single-sample VCF containing
                        transcript, Wildtype protein sequence, and Downstream
                        protein sequence information
  peptide_sequence_length
                        Length of the peptide sequence to use when creating
                        the FASTA.
  output_file           The output fasta file

optional arguments:
  -h, --help            show this help message and exit
  -d DOWNSTREAM_SEQUENCE_LENGTH, --downstream-sequence-length DOWNSTREAM_SEQUENCE_LENGTH
                        Cap to limit the downstream sequence length for
                        frameshifts when creating the fasta file. Use 'full'
                        to include the full downstream sequence. Default: 1000