Additional Commands¶
To make using pVACvector easier, several convenience methods are included in the package.
Creating Vector Visualization¶
By default, pVACvector will create a visualization of the vector design result. For this to happen, the DISPLAY environment variable has to be set. This is often not the case, for example, when running pVACvector on a compute cluster. We provide this convenience method to create the visualization graphic from a successful pVACvector result FASTA file on any machine that has the DISPLAY environment variable set.
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: pvacvector visualize [-h] [-s SPACERS] input_fasta output_directory
Create a visualization of the vector from a pVACvector result fasta
positional arguments:
input_fasta A pVACvector result FASTA file to visualize
output_directory The output directory to save the visualization graphic
to
optional arguments:
-h, --help show this help message and exit
-s SPACERS, --spacers SPACERS
Comma-separated list of peptides that are used as
spacers in the pVACvector result fasta file (default:
AAY,HHHH,GGS,GPGPG,HHAA,AAL,HH,HHC,HHH,HHHD,HHL,HHHC)
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: pvacvector 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¶
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: pvacvector 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: pvacvector 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: `pvacvector
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: pvacvector 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: pvacvector 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)