Additional Commands

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

Download Example Data

usage: pvacfuse 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: pvacfuse valid_alleles [-h]
                              [-p {BigMHC_EL,BigMHC_IM,DeepImmuno,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,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 {BigMHC_EL,BigMHC_IM,DeepImmuno,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PickPocket,SMM,SMMPMBEC,SMMalign}, --prediction-algorithm {BigMHC_EL,BigMHC_IM,DeepImmuno,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,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 Valid Algorithms

usage: pvacfuse valid_algorithms [-h] [-a ALLELE]
                                 [-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 algorithms supported given the specified species and/or allele

optional arguments:
  -h, --help            show this help message and exit
  -a ALLELE, --allele ALLELE
                        Show valid algorithms for the selected allele. For a
                        list of available alleles, use: `pvacfuse
                        valid_alleles`. (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 algorithms for the selected species only
                        (default: None)

List Allele-Specific Cutoffs

usage: pvacfuse 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)