def orforflistmatch(s_orf,orflist):
"""
Which annotations associated with s_orf are significantly overrepresented in orflist?
"""
if not _orfs_by_go: load_GO()
norfs = len(orflist)
totorfs = len(_gos_by_orf.keys())
categories = []
for anno in annotations(s_orf):
categories.append(anno.desc)
sigs = []
for category in categories:
all_by_cat = annotation2orfs(category)
nall = len(all_by_cat)
fracall = float(nall)/float(totorfs)
sub_by_cat = [x for x in orflist if x in all_by_cat]
nsub = len(sub_by_cat)
if norfs == 0: fracsub = 0
else: fracsub = float(nsub)/float(norfs)
sig = Arith.hypgeomsummore(nall,totorfs,norfs,nsub)
sigs.append( (sig, category, fracall, fracsub, sub_by_cat) )
#if s_orf == SGD.gene2orf('NRG1'):
# print '@ NRG1 %5.2e %-40s %4d %4d %4d %4d '%(
# sig,category,nall,totorfs,norfs,nsub)
sigs.sort()
#for sig in sigs: print sig
return sigs
def orflist2categories_long(orflist,thresh=0.05):
"""
Which categories are overrepresented among orflist. Thresh is applied after Bonferroni
correction.
Returns: Sorted list of tuples, [(signifance, category, fracall, fracsub, orflist), ...]
"""
if not _orfs_by_go: load_GO()
norfs = len(orflist)
totorfs = len(_gos_by_orf.keys())
#Determine which categories are described by the set
categories = []
for orf in orflist:
for anno in annotations(orf):
if anno.desc not in categories:
categories.append(anno.desc)
totcats = float(len(categories))
sigs = []
for category in categories:
all_by_cat = annotation2orfs(category)
nall = len(all_by_cat)
fracall = float(nall)/float(totorfs)
sub_by_cat = [x for x in orflist if x in all_by_cat]
nsub = len(sub_by_cat)
fracsub = float(nsub)/float(norfs)
sig = Arith.hypgeomsummore(nall,totorfs,norfs,nsub) * totcats
#print category,sig,nall,totorfs,norfs,nsub,' ',totcats
sigs.append( (sig, category, fracall, fracsub, sub_by_cat) )
sigs.sort()
ans = []
for sigdata in sigs:
sig, category, fracall, fracsub, orfs = sigdata
if sig > thresh: continue
ans.append(sigdata)
return ans
def probOvlp(A,B,thresh=0.7,verbose=None):
if A.width >= B.width:
Wide, Narrow = A, B
else:
Wide, Narrow = B, A
RC = MotifTools.revcomplement
if 1:
newWide = Wide[-1,Wide.width+1]
if Wide.__dict__.has_key('bestWide'):
bestWide = Wide.bestWide
else:
bestWideD = {}
for x in newWide.bestseqs(thresh*newWide.maxscore):
bestWideD[x] = 1
for x in bestWideD.keys():
bestWideD[RC(x)] = 1
Wide.bestWide = bestWideD.keys()
bestWide = Wide.bestWide
Wide = newWide
if Narrow.__dict__.has_key('bestNarrow'):
bestNarrow = Narrow.bestNarrow
else:
bestNarrowD = {}
for x in Narrow.bestseqs(thresh*Narrow.maxscore):
bestNarrowD[x] = 1
for x in bestNarrowD.keys():
bestNarrowD[RC(x)] = 1
bestNarrow = bestNarrowD.keys()
Narrow.bestNarrow = bestNarrow
#bestWide = [x[1] for x in Wide.bestseqs (thresh*Wide.maxscore) ]
#bestNarrow = [x[1] for x in Narrow.bestseqs(thresh*Narrow.maxscore)]
countNarrow = len(bestNarrow)
countWide = len(bestWide)
numtotal = math.pow(4,Wide.width)
fudgefactor = math.pow(4,Wide.width - Narrow.width)
bestWideTups = [(x,MotifTools.revcomplement(x)) for x in bestWide]
countBoth = 0
for i in range(len(bestNarrow)):
m_narrow = bestNarrow[i]
delj = []
for j in range(len(bestWideTups)):
if (bestWideTups[j][0].find(m_narrow) >= 0) or (bestWideTups[j][1].find(m_narrow) >= 0):
countBoth += 1
delj.append(j)
delj.reverse() #Chew in from the back
for j in delj:
del(bestWideTups[j])
if verbose: print '%10d %10d %10d %10d | %10d %5d '%(
countWide, numtotal, countNarrow *fudgefactor , countBoth , countNarrow, Wide.width - Narrow.width),
p = Arith.hypgeomsummore(countWide, #Num Interesting
numtotal, #All k-mers
countNarrow * fudgefactor, #Number picked
countBoth ) #Number found
return p
def probOvlp(A, B, thresh=0.7, verbose=None):
if A.width >= B.width:
Wide, Narrow = A, B
else:
Wide, Narrow = B, A
RC = MotifTools.revcomplement
if 1:
newWide = Wide[-1, Wide.width + 1]
if Wide.__dict__.has_key('bestWide'):
bestWide = Wide.bestWide
else:
bestWideD = {}
for x in newWide.bestseqs(thresh * newWide.maxscore):
bestWideD[x] = 1
for x in bestWideD.keys():
bestWideD[RC(x)] = 1
Wide.bestWide = bestWideD.keys()
bestWide = Wide.bestWide
Wide = newWide
if Narrow.__dict__.has_key('bestNarrow'):
bestNarrow = Narrow.bestNarrow
else:
bestNarrowD = {}
for x in Narrow.bestseqs(thresh * Narrow.maxscore):
bestNarrowD[x] = 1
for x in bestNarrowD.keys():
bestNarrowD[RC(x)] = 1
bestNarrow = bestNarrowD.keys()
Narrow.bestNarrow = bestNarrow
#bestWide = [x[1] for x in Wide.bestseqs (thresh*Wide.maxscore) ]
#bestNarrow = [x[1] for x in Narrow.bestseqs(thresh*Narrow.maxscore)]
countNarrow = len(bestNarrow)
countWide = len(bestWide)
numtotal = math.pow(4, Wide.width)
fudgefactor = math.pow(4, Wide.width - Narrow.width)
bestWideTups = [(x, MotifTools.revcomplement(x)) for x in bestWide]
countBoth = 0
for i in range(len(bestNarrow)):
m_narrow = bestNarrow[i]
delj = []
for j in range(len(bestWideTups)):
if (bestWideTups[j][0].find(m_narrow) >=
0) or (bestWideTups[j][1].find(m_narrow) >= 0):
countBoth += 1
delj.append(j)
delj.reverse() #Chew in from the back
for j in delj:
del (bestWideTups[j])
if verbose:
print '%10d %10d %10d %10d | %10d %5d ' % (
countWide, numtotal, countNarrow * fudgefactor, countBoth,
countNarrow, Wide.width - Narrow.width),
p = Arith.hypgeomsummore(
countWide, #Num Interesting
numtotal, #All k-mers
countNarrow * fudgefactor, #Number picked
countBoth) #Number found
return p
