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):