def getAlt3Conservation(msa,cm,cluster_id,start,stop1,stop2,**kwargs):
gene=genomic_seq[cluster_id] # BARMAK'S GENOMIC FRAGMENT
ss1=listUnion(cm[gene[stop1:stop1+2]]) # SPLICE SITES ON hg17
ss2=listUnion(cm[gene[stop2:stop2+2]])
ss3=listUnion(cm[gene[start-2:start]])
e1=ss1+ss2 # GET INTERVAL BETWEEN PAIR OF SPLICE SITES
e2=listUnion(cm[gene[start:min(stop1,stop2)]])
getSSMap(msa,ss1,ss2,ss3,e1,e2,cluster_id=cluster_id,**kwargs)
def getAlt5Conservation(msa,cm,cluster_id,start1,start2,stop,**kwargs):
gene=genomic_seq[cluster_id] # BARMAK'S GENOMIC FRAGMENT
ss1=listUnion(cm[gene[start1-2:start1]]) # SPLICE SITES ON hg17
ss2=listUnion(cm[gene[start2-2:start2]])
ss3=listUnion(cm[gene[stop:stop+2]])
e1=ss1+ss2 # GET INTERVAL BETWEEN PAIR OF SPLICE SITES
e2=listUnion(cm[gene[max(start1,start2):stop]])
getSSMap(msa,ss1,ss2,ss3,e1,e2,cluster_id=cluster_id,**kwargs)
