nerve,

Looking at the things you want done, I don't see how code can tell that

GeneX,GeneY,GeneP,spc1,spc2 
GeneY,spc3,spc4 
GeneZ,spc3,spc4
[download]

Should lead to:

Desired Result 
GeneX,GeneY,GeneP,GeneZ,spc1=1,spc2=1,spc3=2,spc4=2
[download]

What in the data set "says" that GeneZ is to be clustered with X, Y, and P? Nothing that I can determine. The counts (e.g. spc1=1, etc) would be easy to do and the code I presented creates a stack of spc results. Just pop results off the stack, and count instances.

David.