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Optional Downstream Analysis Tools

Generate Protein Fasta

Using TensorFlow backend.
/home/docs/checkouts/readthedocs.org/user_builds/pvactools/conda/latest/lib/python3.5/site-packages/requests/__init__.py:91: RequestsDependencyWarning: urllib3 (1.24.1) or chardet (3.0.4) doesn't match a supported version!
  RequestsDependencyWarning)
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

Generate Condensed, Ranked Report

Using TensorFlow backend.
/home/docs/checkouts/readthedocs.org/user_builds/pvactools/conda/latest/lib/python3.5/site-packages/requests/__init__.py:91: RequestsDependencyWarning: urllib3 (1.24.1) or chardet (3.0.4) doesn't match a supported version!
  RequestsDependencyWarning)
usage: pvacseq generate_condensed_ranked_report [-h] [-m {lowest,median}]
                                                input_file output_file

positional arguments:
  input_file            A pVACseq .all_epitopes.tsv or .filtered.tsv report
                        file
  output_file           The file path to write the condensed, ranked report
                        tsv to

optional arguments:
  -h, --help            show this help message and exit
  -m {lowest,median}, --top-score-metric {lowest,median}
                        The ic50 scoring metric to use for ranking epitopes by
                        binding-threshold and minimum fold change. lowest:
                        Best MT Score/Corresponding Fold Change - lowest MT
                        ic50 binding score/corresponding fold change of all
                        chosen prediction methods. median: Median MT
                        Score/Median Fold Change - median MT ic50 binding
                        score/fold change of all chosen prediction methods.
                        Default: median