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Additional Commands

To make using pVACvector easier, several convenience methods are included in the package.

Download Example Data

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: pvacfuse download_example_data [-h] destination_directory

positional arguments:
  destination_directory
                        Directory for downloading example data

optional arguments:
  -h, --help            show this help message and exit

List Valid Alleles

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: pvacfuse valid_alleles [-h]
                              [-p {MHCflurry,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}]

optional arguments:
  -h, --help            show this help message and exit
  -p {MHCflurry,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}, --prediction-algorithm {MHCflurry,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}
                        The epitope prediction algorithms to use

List Allele-Specific Cutoffs

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: pvacvector allele_specific_cutoffs [-h] [-a ALLELE]

optional arguments:
  -h, --help            show this help message and exit
  -a ALLELE, --allele ALLELE
                        The allele to use