🔎

    Additional Arguments

    In addition, to the arguments described in previous sections (Binding Predictions and Cohort), detailed descriptions of the remaining arguments are:

    -o or --output

    Specifies the output directory where all the results will be stored. This is a required argument. If the directory does not exist, it will be created.

    -i or --index

    Required only when -c or --cohort is provided.

    Each genotype in the cohort will be compared to this allele. Multiple index alleles can be provides as space delimited values (e.g. -i A02:01 C08:01).

    -m or --measure

    In addition, to the default calculations based on TCR/KIR interaction positions it is possible to provide a custom motif and name. All calculations will also be performed for the supplied measures.

    One or multiple measures can be provided as Name:pos,pos,pos...

    For example -m Example1:1,2,3 Example2:4,5,6, will produce additional entries in the output for measures named Example1 and Example2 based on the specified peptide positions/motifs.

    --drop-default

    If this flag is supplied, no calculations will be made on default motifs representing the TCR and KIR "interaction space".

    -p or --peptide-length

    By default only 9-mer peptides are used for calculations. However, it is also possible to perform separate calculation for each k-mer as long as it is present in the binding predictions.

    Multiple peptide lengths can be supplied at the same time as -p 8 9 10 11, which will perform independent calculation for each of the 4 k-mer sizes.

    -u or --unique

    If the same motif occurs across diferent bound peptides for a given allele, they will be counted/considered only once.

    --prefix

    This will prepend a identifier of choice to all the output files. This is useful if you want to name the outputs after the specific cohort and proteome combination (e.g. --prefix HTLV_RandomCohort).

    --threads

    By default 4 threads are used for calculations but more can be provided, for very large proteomes this will make significant speed improvements if increased.

    --update

    This flag will ensure that new EBI kir ligand motif data is downloaded before any calculations.