Helper Tools¶
This section describes a set of utility tools designed to assist users in working more efficiently with the core functionality of the software. These helper tools provide streamlined workflows, support data formatting and validation, and simplify common post-processing steps. Our comparison tool and others included here can help users compare results, generate reports, and prepare data for further analysis.
Download WDL tool wrappers¶
Workflow Description Language (WDL) tool wrappers for pVACseq and pVACfuse
can be downloaded using the pvactools download_wdls command.
usage: pvactools download_wdls [-h] destination_directory
Download pVACtools WDLs to run the main pVACseq and pVACfuse pipelines
positional arguments:
destination_directory
Directory for downloading WDLs
optional arguments:
-h, --help show this help message and exit
Download CWL tool wrappers¶
Common Workflow Language (CWL) tool wrappers for pVACseq, pVACfuse, and
pVACvector can be downloaded using the pvactools download_cwls command.
usage: pvactools download_cwls [-h] destination_directory
Download pVACtools CWLs for each tool's main pipeline
positional arguments:
destination_directory
Directory for downloading CWLs
optional arguments:
-h, --help show this help message and exit
List Valid Alleles¶
usage: pvactools valid_alleles [-h]
[-p {BigMHC_EL,BigMHC_IM,DeepImmuno,ImmuScope_IM,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,MixMHC2pred,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}]
[-l {8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30}]
Show a list of valid allele names
optional arguments:
-h, --help show this help message and exit
-p {BigMHC_EL,BigMHC_IM,DeepImmuno,ImmuScope_IM,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,MixMHC2pred,MixMHCpred,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PRIME,PickPocket,SMM,SMMPMBEC,SMMalign}, --prediction-algorithm {BigMHC_EL,BigMHC_IM,DeepImmuno,ImmuScope_IM,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,MixMHC2pred,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)
-l {8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30}, --length {8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30}
Show valid alleles for the selected length only
(default: None)
List Valid Algorithms¶
usage: pvactools 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: `pvactools
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¶
usage: pvactools valid_netmhcpan_versions [-h]
Show a list of valid versions of NetMHCIIpan and NetMHCIIpanEL that can be
used.
optional arguments:
-h, --help show this help message and exit
List Allele-Specific Cutoffs¶
usage: pvactools 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)