def find_entry_score(ln, l, aliFormat, pScoreCutoff):
mxBitSc = 700
sigma2 = 3
skipFlag = False
if (aliFormat == 0): # gnu-sam
pScore = float(l[12].split(':')[2])
if (pScore < pScoreCutoff):
skipFlag = True
elif (aliFormat == 1): # sam
pScore = samUtils.findSamAlignScore(l)
if pScore is None:
mapq = float(l[4])
mapq2 = mapq / (-10.0)
pScore = 1.0 - pow(10, mapq2)
if (pScore < pScoreCutoff):
skipFlag = True
elif (aliFormat == 2): # bl8
eVal = float(l[10])
if (eVal > pScoreCutoff):
skipFlag = True
bitSc = float(l[11]) / sigma2
if bitSc > mxBitSc:
bitSc = mxBitSc
pScore = math.exp(bitSc)
#pScore = int(round(pScore*100)) # Converting to integer to conserve memory space
#if pScore < 1:
# skipFlag = true
return (pScore, skipFlag)
def find_entry_score(ln, l, aliFormat, pScoreCutoff):
mxBitSc = 700
sigma2 = 3
skipFlag = False
if (aliFormat == 0): # gnu-sam
pScore = float(l[12].split(':')[2])
if (pScore < pScoreCutoff):
skipFlag = True
elif (aliFormat == 1): # sam
pScore = samUtils.findSamAlignScore(l)
if pScore is None:
mapq = float(l[4])
mapq2 = mapq/(-10.0)
pScore = 1.0 - pow(10,mapq2)
if (pScore < pScoreCutoff):
skipFlag = True
elif (aliFormat == 2): # bl8
eVal = float(l[10])
if (eVal > pScoreCutoff):
skipFlag = True
bitSc = float(l[11])/sigma2
if bitSc > mxBitSc:
bitSc = mxBitSc
pScore = math.exp(bitSc)
#pScore = int(round(pScore*100)) # Converting to integer to conserve memory space
#if pScore < 1:
# skipFlag = true
return (pScore, skipFlag)
def extractRead(appendAlignFile, readFile):
h_readId = {}
with open(appendAlignFile,'r') as in1:
with open(readFile,'w') as out1:
for ln in in1:
if (ln[0] == '@' or ln[0] == '#'):
continue
l = ln.split('\t')
aScore = samUtils.findSamAlignScore(l)
if (aScore is None):
continue
readId=l[0]
score = h_readId.get(readId,None)
if (score is None):
h_readId[readId] = aScore
sequence = l[9]
quality = l[10]
out1.write('@%s\n%s\n+\n%s\n' % (readId, sequence, quality))
def extractRead(appendAlignFile, readFile):
h_readId = {}
with open(appendAlignFile, 'r') as in1:
with open(readFile, 'w') as out1:
for ln in in1:
if (ln[0] == '@' or ln[0] == '#'):
continue
l = ln.split('\t')
aScore = samUtils.findSamAlignScore(l)
if (aScore is None):
continue
readId = l[0]
score = h_readId.get(readId, None)
if (score is None):
h_readId[readId] = aScore
sequence = l[9]
quality = l[10]
out1.write('@%s\n%s\n+\n%s\n' %
(readId, sequence, quality))