Additional Commands

To make using pVAC-Seq easier several convenience methods are included in the package.

Download Example Data

usage: pvacseq download_example_data [-h] destination_directory

Positional Arguments

destination_directory
	Directory for downloading example data

Install VEP Plugin

usage: pvacseq install_vep_plugin [-h] vep_plugins_path

Positional Arguments

vep_plugins_path
	Path to your VEP_plugins directory

List Valid Alleles

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

Named Arguments

-p, –prediction-algorithm
	Possible choices: NNalign, NetMHC, NetMHCIIpan, NetMHCcons, NetMHCpan, PickPocket, SMM, SMMPMBEC, SMMalign The epitope prediction algorithms to use

Documentation For Configuration Files

usage: pvacseq config_files [-h] {additional_input_file_list}

Positional Arguments

config_file_type
	Possible choices: additional_input_file_list The config file type to retrieve more information for