PIQUE does not automatically analyse all sub-groups

[tony-travis]

The current version of PIQUE does not automatically analyse ALL subgroups.

At present we use a "bash" for loop to analyse ALL sub-groups e.g.:

cd test
make group
wget --no-check-certificate  http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip
unzip RiceDiversity.44K.MSU6.Genotypes_PLINK.zip
mv -i ./RiceDiversity_44K_Genotypes_PLINK/sativas* .
rmdir RiceDiversity_44K_Genotypes_PLINK
rm RiceDiversity.44K.MSU6.Genotypes_PLINK.zip
pique-input -d -v -i sativas413 -o sativas_group_GWAS -p rice_phenotype_group.txt -k -c -e 5
pique-run -d -v -i sativas_group_GWAS -k IBS -c sativas_group_GWAS.covar -n 16
for group in ADMIX AUS IND TEJ TRJ; do \
    prefix=sativas_group_GWAS\_$group; \
    pique-run -d -v -i $prefix -k IBS -n 16; \
done

[ghost]

It's analyse a specific groups🙄