function output=assess_vec_CC_b(input,whichgenes)
%output=assess_vec_CC_b(input,whichgenes)

input=full(input);
whichgenes=full(whichgenes);
  whichgenes=logical(whichgenes);
path(path,'/home/jesse')

load /home/jesse/psdstuff/GOgenemat

load /home/jesse/psdstuff/genelist

  GOgenemat=GOgenemat(whichgenes,:);


ranks=tiedrank(input);
ROC_using_sorted=nan(size(GOgenemat,2),1);

for m=1:10127
  TF=logical(GOgenemat(:,m));
  TF=full(TF');
if sum(TF)>=20 & sum(TF)<=1000
fulllabels=TF;
    badlabels=(fulllabels==0);
numingoer=sum(fulllabels);
its=full(floor(sum(badlabels)/numingoer));
badlabels=find(badlabels);
goodlabels=find(fulllabels);
badlabels=badlabels(randperm(length(badlabels)));
labels=[ones(numingoer,1);zeros(numingoer,1)];
output=0;
for i=1:its
  temp_input=input([goodlabels badlabels((1+(its-1)*numingoer):(its*numingoer))]);
  temp_gene_list_n=gene_list_n([goodlabels badlabels((1+(its-1)*numingoer):(its*numingoer))]);
[r,k]=sort(temp_input,'descend');
sorted_gene_list_n=temp_gene_list_n(k);
indices=TF([goodlabels badlabels((1+(its-1)*numingoer):(its*numingoer))]);
fraction_estimate=labels(randperm(length(labels)));
fraction_estimate=sum(fraction_estimate(1:round(end/2))); %not actually a fraction
output1=(sum(indices(k(1:round(fraction_estimate*2))))+sum(~indices(k((round(fraction_estimate*2)+1):end))))/sum(indices)/2;

output=output+output1;

end
output=output/its;
    
    ROC_using_sorted(m)=output;
end
end


output=ROC_using_sorted;