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.
usage: pvacvector visualize [-h] [-s SPACERS] input_fasta output_directory
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¶
usage: pvacvector download_example_data [-h] destination_directory
positional arguments:
destination_directory
Directory for downloading example data
optional arguments:
-h, --help show this help message and exit
List Valid Alleles¶
usage: pvacvector valid_alleles [-h]
[-p {MHCflurry,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}]
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}
The epitope prediction algorithms to use (default:
None)
List Allele-Specific Cutoffs¶
usage: pvacvector allele_specific_cutoffs [-h] [-a ALLELE]
optional arguments:
-h, --help show this help message and exit
-a ALLELE, --allele ALLELE
The allele to use (default: None)