Additional Commands

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

Creating Vector Visualization

By default, pVACvector will create a visualization of the vector design result. For this to happen, the DISPLAY environment variable has to be set. This is often not the case, for example, when running pVACvector on a compute cluster. We provide this convenience method to create the visualization graphic from a successful pVACvector result FASTA file on any machine that has the DISPLAY environment variable set.

usage: pvacvector visualize [-h] [-s SPACERS] input_fasta output_directory

Create a visualization of the vector from a pVACvector result fasta

positional arguments:
  input_fasta           A pVACvector result FASTA file to visualize
  output_directory      The output directory to save the visualization graphic
                        to

optional arguments:
  -h, --help            show this help message and exit
  -s SPACERS, --spacers SPACERS
                        Comma-separated list of peptides that are used as
                        spacers in the pVACvector result fasta file (default:
                        AAY,HHHH,GGS,GPGPG,HHAA,AAL,HH,HHC,HHH,HHHD,HHL,HHHC)

Download Example Data

usage: pvacvector download_example_data [-h] destination_directory

Download example input and output files

positional arguments:
  destination_directory
                        Directory for downloading example data

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

List Valid Alleles

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

Show a list of valid allele names

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 (default:
                        None)

List Allele-Specific Cutoffs

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

Show the allele specific cutoffs

optional arguments:
  -h, --help            show this help message and exit
  -a ALLELE, --allele ALLELE
                        The allele to use (default: None)