pVACseq logo

Additional Commands

To make using pVACseq 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: pvacseq 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

Install VEP Plugin

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 install_vep_plugin [-h] vep_plugins_path

positional arguments:
  vep_plugins_path  Path to your VEP_plugins directory

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

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

Documentation For Configuration Files

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 config_files [-h] {additional_input_file_list}

positional arguments:
  {additional_input_file_list}
                        The config file type to retrieve more information for

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