Example dataset for running pastrami
## This toy example assumes that the Pastrami script is on your PATH
## We assume that the HapMap recombination maps are present in the directory hap_map
## A directory where the Pastrami output will be written
mkdir toy_results
## Create the haplotypes from the linkage map
pastrami.py hapmake --map-dir hap_map --min-snps 3 --max-snps 10 --max-rate 0.2 --haplotypes toy_results/haps.haps
## Build the reference set copying values
pastrami.py build --hap toy_results/haps.haps --reference-pickle toy_results/reference.pickle --reference-prefix toy/reference --reference-out toy/reference.tsv --threads 32
## Compare the query set to the reference set
pastrami.py query --reference-pickle toy_results/reference.pickle --query-prefix toy/query --query-out toy_results/query.tsv --combined-out toy_results/combined.tsv --threads 30
## Aggregate the copying vectors into ancestry fractions across population groups
pastrami.py aggregate --pastrami-output toy_results/combined.tsv --pop-group toy/pop_group.txt --pastrami-fam toy/combined.fam --out-prefix toy_results/combined