pVACseq logo

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

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

Install VEP Plugin

usage: pvacseq install_vep_plugin [-h] vep_plugins_path

Install the Wildtype and Frameshift VEP plugins into your VEP_plugins
directory

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}]
                             [-s {atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,Geoffroy's tamarin,golden lion tamarin,gorilla,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,olive baboon,pig,rainbow trout,rhesus macaque,sheep,southern pig-tailed macaque,stump-tailed macaque,white-faced saki,white-fronted spider monkey,yellow baboon}]

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}
                        Show valid alleles for the selected prediction
                        algorithm only (default: None)
  -s {atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,Geoffroy's tamarin,golden lion tamarin,gorilla,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,olive baboon,pig,rainbow trout,rhesus macaque,sheep,southern pig-tailed macaque,stump-tailed macaque,white-faced saki,white-fronted spider monkey,yellow baboon}, --species {atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,Geoffroy's tamarin,golden lion tamarin,gorilla,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,olive baboon,pig,rainbow trout,rhesus macaque,sheep,southern pig-tailed macaque,stump-tailed macaque,white-faced saki,white-fronted spider monkey,yellow baboon}
                        Show valid alleles for the selected species only
                        (default: human)

List Allele-Specific Cutoffs

usage: pvacseq 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)