def rows():
'''takes xml blast file and returns a generator of best
pairwise results
'''
hg=B.ncbiXmlHitGenerator(iFile)
pairCache={}
canCache={}
i=0
for rec in hg:
i+=1
seqID=int(rec['def'])
#1st variable foundandidate_Sequence_Energy
canName=rec['query-def']
#2nd variable found
qseq=rec['hsps'][0]['qseq']
hseq=rec['hsps'][0]['hseq']
rqseq=B.reverseComplement(qseq)
en=A.energy(hseq,rqseq)
#3rd variable found
try:
canID=canCache[canName]
except KeyError:
canCache[canName]=Candidate(canName).ID()
canID=canCache[canName]
#timesaver so we only have to look it up once
try:
if en < pairCache[canID,seqID]:
pairCache[canID,seqID]=en
except KeyError:
pairCache[canID,seqID]=en
#store the most negative value for the pair
for canID,seqID in pairCache.iterkeys():
rv=[canID,seqID,pairCache[canID,seqID]]
yield rv
def rows():
'''
'''
canCache={}
pairCache={}
lastCanName=''
hg=B.ncbiXmlHitGenerator(iFile)
i=0
for rec in hg:
i+=1
seqID=int(rec['def'])
#1st variable found
canName=rec['query-def']
#2nd variable found
if canName!=lastCanName:
for tID,canID in pairCache.iterkeys():
min_E=min(pairCache[tID,canID])
max_E=max(pairCache[tID,canID])
mean_E=N.mean(pairCache[tID,canID])
SD_E=N.std(pairCache[tID,canID])
N_E=0
N_E30=0
N_E40=0
N_E50=0
N_E100=0
for ener in pairCache[tID,canID]:
N_E+=1
if ener<=-30:
N_E30+=1
if ener<=-40:
N_E40+=1
if ener<=-50:
N_E50+=1
if ener<=-100:
N_E100+=1
rv=[canID,tID,min_E,max_E,mean_E,SD_E,N_E,N_E30,N_E40,
N_E50,N_E100]
yield rv
pairCache={}
lastCanName=canName
#stores and refreshes dictionary
#once we have moved onto next pair
try:
canID=canCache[canName]
except KeyError:
canCache[canName]=Candidate(canName).ID()
canID=canCache[canName]
#timesaver so we only have to look it up once
if canID%4!=0:
continue
#hit=str(rec)
#3rd variable found
qseq=rec['hsps'][0]['qseq']
hseq=rec['hsps'][0]['hseq']
rqseq=B.reverseComplement(qseq)
en=A.energy(hseq,rqseq)
#3rd variable found
for t in Sequence(seqID).taxa():
tID=t.ID()
try:
pairCache[tID,canID].append(en)
except KeyError:
pairCache[tID,canID]=[en]
#checks to see if energy is most negative for the pair
#replaces old result if it is
for tID,canID in pairCache.iterkeys():
min_E=min(pairCache[tID,canID])
max_E=max(pairCache[tID,canID])
mean_E=N.mean(pairCache[tID,canID])
SD_E=N.std(pairCache[tID,canID])
N_E=0
N_E30=0
N_E40=0
N_E50=0
N_E100=0
for ener in pairCache[tID,canID]:
N_E+=1
if ener<=-30:
N_E30+=1
if ener<=-40:
N_E40+=1
if ener<=-50:
N_E50+=1
if ener<=-100:
N_E100+=1
rv=[canID,tID,min_E,max_E,mean_E,SD_E,N_E,N_E30,N_E40,
N_E50,N_E100]
yield rv
