Additional Commands

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

Download Example Data

Creating converter from 7 to 5
Creating converter from 5 to 7
Creating converter from 7 to 5
Creating converter from 5 to 7
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

Creating converter from 7 to 5
Creating converter from 5 to 7
Creating converter from 7 to 5
Creating converter from 5 to 7
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

Creating converter from 7 to 5
Creating converter from 5 to 7
Creating converter from 7 to 5
Creating converter from 5 to 7
usage: pvacseq valid_alleles [-h]
                             [-p {BigMHC_EL,BigMHC_IM,DeepImmuno,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,MixMHCpred,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PRIME,PickPocket,SMM,SMMPMBEC,SMMalign}]
                             [-s {assam macaque,atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chicken,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,domestic yak,eastern gorilla,Geoffroy's tamarin,golden lion tamarin,gorilla,green monkey,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,northern pig-tailed macaque,norway rat,olive baboon,pig,rainbow trout,rhesus macaque,sheep,sooty mangabey,southern pig-tailed macaque,stump-tailed macaque,sumatran orangutan,three-striped night monkey,tibetan macaque,vervet monkey,white-faced saki,white-fronted spider monkey,white-lipped tamarin,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,MixMHCpred,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PRIME,PickPocket,SMM,SMMPMBEC,SMMalign}, --prediction-algorithm {BigMHC_EL,BigMHC_IM,DeepImmuno,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,MixMHCpred,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PRIME,PickPocket,SMM,SMMPMBEC,SMMalign}
                        Show valid alleles for the selected prediction
                        algorithm only (default: None)
  -s {assam macaque,atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chicken,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,domestic yak,eastern gorilla,Geoffroy's tamarin,golden lion tamarin,gorilla,green monkey,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,northern pig-tailed macaque,norway rat,olive baboon,pig,rainbow trout,rhesus macaque,sheep,sooty mangabey,southern pig-tailed macaque,stump-tailed macaque,sumatran orangutan,three-striped night monkey,tibetan macaque,vervet monkey,white-faced saki,white-fronted spider monkey,white-lipped tamarin,yellow baboon}, --species {assam macaque,atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chicken,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,domestic yak,eastern gorilla,Geoffroy's tamarin,golden lion tamarin,gorilla,green monkey,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,northern pig-tailed macaque,norway rat,olive baboon,pig,rainbow trout,rhesus macaque,sheep,sooty mangabey,southern pig-tailed macaque,stump-tailed macaque,sumatran orangutan,three-striped night monkey,tibetan macaque,vervet monkey,white-faced saki,white-fronted spider monkey,white-lipped tamarin,yellow baboon}
                        Show valid alleles for the selected species only
                        (default: human)

List Valid Algorithms

Creating converter from 7 to 5
Creating converter from 5 to 7
Creating converter from 7 to 5
Creating converter from 5 to 7
usage: pvacseq valid_algorithms [-h] [-a ALLELE]
                                [-s {assam macaque,atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chicken,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,domestic yak,eastern gorilla,Geoffroy's tamarin,golden lion tamarin,gorilla,green monkey,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,northern pig-tailed macaque,norway rat,olive baboon,pig,rainbow trout,rhesus macaque,sheep,sooty mangabey,southern pig-tailed macaque,stump-tailed macaque,sumatran orangutan,three-striped night monkey,tibetan macaque,vervet monkey,white-faced saki,white-fronted spider monkey,white-lipped tamarin,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: `pvacseq
                        valid_alleles`. (default: None)
  -s {assam macaque,atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chicken,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,domestic yak,eastern gorilla,Geoffroy's tamarin,golden lion tamarin,gorilla,green monkey,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,northern pig-tailed macaque,norway rat,olive baboon,pig,rainbow trout,rhesus macaque,sheep,sooty mangabey,southern pig-tailed macaque,stump-tailed macaque,sumatran orangutan,three-striped night monkey,tibetan macaque,vervet monkey,white-faced saki,white-fronted spider monkey,white-lipped tamarin,yellow baboon}, --species {assam macaque,atlantic salmon,black-headed spider monkey,blue monkey,bonobo,bornean orangutan,brown-mantled tamarin,chicken,chimpanzee,common marmoset,common squirrel monkey,cottontop tamarin,cow,crab-eating macaque,dog,domestic yak,eastern gorilla,Geoffroy's tamarin,golden lion tamarin,gorilla,green monkey,grivet,hamadryas baboon,horse,human,lar gibbon,mouse,moustached tamarin,northern pig-tailed macaque,norway rat,olive baboon,pig,rainbow trout,rhesus macaque,sheep,sooty mangabey,southern pig-tailed macaque,stump-tailed macaque,sumatran orangutan,three-striped night monkey,tibetan macaque,vervet monkey,white-faced saki,white-fronted spider monkey,white-lipped tamarin,yellow baboon}
                        Show valid algorithms for the selected species only
                        (default: None)

List Valid NetMHCIIpan/NetMHCIIpanEL Versions

Creating converter from 7 to 5
Creating converter from 5 to 7
Creating converter from 7 to 5
Creating converter from 5 to 7
usage: pvacseq valid_netmhcpan_versions [-h] [-l]

Show a list of valid versions of NetMHCIIpan and NetMHCIIpanEL that can be
used.

optional arguments:
  -h, --help  show this help message and exit
  -l, --list  List the valid NetMHCIIpan and NetMHCIIpanEL versions. (default:
              None)

List Allele-Specific Cutoffs

Creating converter from 7 to 5
Creating converter from 5 to 7
Creating converter from 7 to 5
Creating converter from 5 to 7
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)