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
- Required Arguments
destination_directory Directory for downloading example data
Install VEP Plugin¶
usage: pvacseq install_vep_plugin [-h] vep_plugins_path
- Required 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}]
- Optional Arguments
-p, --prediction-algorithm The epitope prediction algorithms to use
Possible choices: NNalign, NetMHC, NetMHCIIpan, NetMHCcons, NetMHCpan, PickPocket, SMM, SMMPMBEC, SMMalign
Documentation For Configuration Files¶
usage: pvacseq config_files [-h] {additional_input_file_list}
- Required Arguments
config_file_type The config file type to retrieve more information for
Possible choices: additional_input_file_list