def geneprobelistmatch(gene,probelist):
if 'Yeast6kArray' not in dir(): from TAMO.DataSources import Yeast6kArray
s_orf = SGD.gene2orf(gene)
orfs = []
for probe in probelist:
orfs.extend(Yeast6kArray.probe2orfs(probe))
#print "%4d --> %4d "%(len(probelist),len(orfs)),
return orforflistmatch(s_orf,orfs)
def cendist(spotname):
"""
Distance from feature (spot) to nearest centromeme
"""
poss = spot_pos(spotname)
if poss:
cendist = min([SGD.dist_from_cen(pos.chr,pos.start,pos.stop) for pos in poss])
return cendist
return -1
def telomeredist(spotname):
"""
Distance from feature (spot) to nearest telomere
"""
poss = spot_pos(spotname)
if poss:
teldist = min([SGD.dist_from_tel(pos.chr,pos.start,pos.stop) for pos in poss])
return teldist
return -1
def gene2annotations(gene): return annotations(SGD.gene2orf(gene)) # List annotations for an ORF def annotations(orf):
