selectvariants.snplist.meta

#!/bin/bash

## PLEASE ONLY ABSOLUTE PATHS

# this stays constant across studies
ensg=$1
shift
prot=$1
shift
condition=$1
shift
outfile=$1
shift
setfile=$1
shift
indexvariant=$1
shift

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

# this is study specific
SS=("$@")
names=()
phenos=()
plinkfiles=()
matrices=()
gdss=()
assocs=()

for ssarg in ${SS[@]}; do
	IFS=',' read -r -a csfields <<< "$ssarg"
		names+=( "${csfields[0]}" )
		phenos+=( "${csfields[1]}" )
		plinkfiles+=( "${csfields[2]}" )
		matrices+=( "${csfields[3]}" )
		gdss+=( "${csfields[4]}" )
		assocs+=( "${csfields[5]}" )
done


for i in ${!SS[@]}; do
	echo study $i is named ${names[$i]} #, has pheno ${phenos[$i]}, plink ${plinkfiles[$i]}, matrix ${matrices[$i]}, gds ${gdss[$i]}, assoc ${assocs[$i]}
done
echo index variant is $indexvariant

mkdir $outfile || exit
 cd $outfile


condsnp=$indexvariant
echo Now conditioning on other cohorts for $condsnp...

for i in ${!SS[@]}; do
		echo Processing cohort "${names[$i]}" ...
		$DIR/selectvariants.snplist $ensg $condition ${phenos[$i]} ${plinkfiles[$i]} ${matrices[$i]} ${gdss[$i]} $setfile $condsnp ${names[$i]}.$prot.$ensg.$condition.${condsnp/:/_}
		if [[ -s ${names[$i]}.$prot.$ensg.$condition.${condsnp/:/_}/tocondition.var.1 ]]; then
			echo ${names[$i]}.$prot.$ensg.$condition.${condsnp/:/_}/tocondition >> toanalyse
		fi
done

echo
echo META ANALYSIS
echo
grep -w '^'$ensg.$condition $setfile | sed 's/\t/-/;s/\t/:/' | grep -w -f <(echo $indexvariant | sed 's/chr//g'| tr ',' '\n') | sed 's/-/\t/;s/:/\t/'>redux.variantset

mfp=$(cat toanalyse | sed 's/^/\"/;s/$/",/'| tr '\n' ' '| sed 's/, $/\n/')
echo $mfp
Rscript -e 'library(GMMAT);library(data.table)
nf='$(cat toanalyse| wc -l)'
print(nf)
mfp=c('"$mfp"')
print(mfp)
meta=SMMAT.meta(meta.files.prefix=mfp, n.files=rep(1, nf),
        group.file="redux.variantset",
        MAF.range=c(1e-10, 0.05),
        MAF.weights.beta = c(1,1),
        miss.cutoff=0.01,
        tests=c("O", "E"),
        rho=(0:10)/10,
        use.minor.allele=T
          )

fwrite(meta, "'$ensg.$prot'.cond.out", sep="\t", na=NA, quote=F)
print(t(meta))'