Additional Commands¶
To make using pVACseq 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
optional arguments:
-h, --help show this help message and exit
Install VEP Plugin¶
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¶
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 (default:
None)
List Allele-Specific Cutoffs¶
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 (default: None)