def find_readsAlignScore(filterAlignFiles):
h_readId = {}
for filterAlignFile in filterAlignFiles:
with open(filterAlignFile, 'r') as in1:
for ln in in1:
if (ln[0] == '@' or ln[0] == '#'):
continue
l = ln.split('\t')
readId = l[0]
aScore = samUtils.findSamAlignHiScore(l)
if aScore is not None:
score = h_readId.get(readId, None)
if (score == None) or (score < aScore):
h_readId[readId] = aScore
return h_readId
def find_readsAlignScore(filterAlignFiles):
h_readId = {}
for filterAlignFile in filterAlignFiles:
with open(filterAlignFile,'r') as in1:
for ln in in1:
if (ln[0] == '@' or ln[0] == '#'):
continue
l = ln.split('\t')
readId=l[0]
aScore = samUtils.findSamAlignHiScore(l)
if aScore is not None:
score = h_readId.get(readId,None)
if (score == None) or (score < aScore):
h_readId[readId] = aScore
return h_readId
def filter_alignment(targetAlignFile, filterAlignFiles, outAlignFile):
h_readId = find_readsAlignScore(filterAlignFiles)
with open(targetAlignFile,'r') as in1:
with open(outAlignFile,'w') as out1:
for ln in in1:
if (ln[0] == '@' or ln[0] == '#'):
out1.write(ln)
continue
l = ln.split('\t')
readId=l[0]
aScore = samUtils.findSamAlignHiScore(l)
if (aScore is not None):
score = h_readId.get(readId, None)
if (score == None) or (score < aScore):
#This read is (not/having low scores) in the filterAlignFiles
out1.write(ln)
return outAlignFile
def filter_alignment(targetAlignFile, filterAlignFiles, outAlignFile):
h_readId = find_readsAlignScore(filterAlignFiles)
with open(targetAlignFile, 'r') as in1:
with open(outAlignFile, 'w') as out1:
for ln in in1:
if (ln[0] == '@' or ln[0] == '#'):
out1.write(ln)
continue
l = ln.split('\t')
readId = l[0]
aScore = samUtils.findSamAlignHiScore(l)
if (aScore is not None):
score = h_readId.get(readId, None)
if (score == None) or (score < aScore):
#This read is (not/having low scores) in the filterAlignFiles
out1.write(ln)
return outAlignFile