def getQualityData(self, inputFname, read_sampling_rate=0.05, quality_score_format='Sanger'):
"""
2011-8-15
"""
sys.stderr.write("Getting base quality data from %s ...\n"%(inputFname))
quality_ls_per_position = []
quality_ls = []
no_of_bases_per_position = []
diNuc2count = {}
diNuc2quality_ls = {}
fname_prefix, fname_suffix = os.path.splitext(inputFname)
if fname_suffix=='.gz': #the input file is gzipped. get the new prefix
import gzip
inf = gzip.open(inputFname, 'rb')
else:
inf = open(inputFname, 'r')
counter = 0
real_counter = 0
for line in inf:
if line[0]=='@': #a new read
counter += 1
coin_toss = random.random()
base_string = inf.next().strip()
inf.next()
quality_string = inf.next().strip()
if coin_toss<=read_sampling_rate:
real_counter += 1
read_length = len(base_string)
if len(quality_ls_per_position)<read_length: # extend quality_ls_per_position to house more data
extraNoOfBases = read_length-len(quality_ls_per_position)
for j in xrange(extraNoOfBases):
quality_ls_per_position.append([])
no_of_bases_per_position.append(0)
for i in range(read_length):
base = base_string[i]
base_quality = quality_string[i]
if quality_score_format=='Illumina1.3':
phredScore = utils.getPhredScoreOutOfSolexaScore(base_quality)
else:
phredScore = ord(base_quality)-33
quality_ls_per_position[i].append(phredScore)
quality_ls.append(phredScore)
if base!='N':
no_of_bases_per_position[i] += 1
if i<read_length-1:
nextBase = base_string[i+1]
if nextBase!='N':
diNuc = base + nextBase
if diNuc not in diNuc2quality_ls:
diNuc2quality_ls[diNuc] = []
diNuc2count[diNuc] = 0
diNuc2quality_ls[diNuc].append(phredScore)
diNuc2count[diNuc] += 1
if counter%5000==0 and self.report:
sys.stderr.write("%s%s\t%s"%('\x08'*80, real_counter, counter))
#if baseCount>10000: #temporary, for testing
# break
del inf
sys.stderr.write("%s/%s reads selected. Done.\n"%(real_counter, counter))
return PassingData(quality_ls_per_position=quality_ls_per_position, quality_ls=quality_ls, \
no_of_bases_per_position=no_of_bases_per_position, diNuc2quality_ls=diNuc2quality_ls, diNuc2count=diNuc2count)
def readFilter(self, readData, pmData=None): """ 2011-8-17 0. get smoothed phred score 1. head trimming 2. tail trimming 3. determine if the read after trimming is still long enough (>=minFinalReadLength) 4. convert low-quality base to N 5. if percentage of Ns is <=maxNPercentage """ base_string = readData.base_string quality_string = readData.quality_string halfWindowSize = getattr(pmData, 'halfWindowSize', 1) read_length = len(base_string) smooth_phred_score_ls = [] phred_score_ls = [] for i in range(read_length): base = base_string[i] base_quality = quality_string[i] if pmData.quality_score_format=='Illumina': phredScore = utils.getPhredScoreOutOfSolexaScore(base_quality) else: phredScore = ord(base_quality)-33 phred_score_ls.append(phredScore) if i>=halfWindowSize: #calculate the smooth quality for base at i-halfWindowSize smooth_start_index = max(i-halfWindowSize*2, 0) smooth_stop_index = i+1 smooth_quality = numpy.median(phred_score_ls[smooth_start_index:smooth_stop_index]) smooth_phred_score_ls.append(smooth_quality) leftOver = len(phred_score_ls)-len(smooth_phred_score_ls) for i in range(leftOver): indexOfInterest = len(smooth_phred_score_ls) smooth_start_index = max(indexOfInterest-halfWindowSize, 0) smooth_stop_index = min(indexOfInterest+halfWindowSize+1, len(phred_score_ls)) smooth_quality = numpy.median(phred_score_ls[smooth_start_index:smooth_stop_index]) smooth_phred_score_ls.append(smooth_quality) badHeadStopIndex = -1 #start from the one before 0 foundBadHeadStop = False badTailStart = len(base_string) #start from the one after the final base foundBadTailStart = False for i in range(read_length): if (foundBadHeadStop and foundBadTailStart) or badHeadStopIndex>=badTailStart: #stop right here break if foundBadHeadStop is False: #check starts from the beginning phredScore = smooth_phred_score_ls[i] if phredScore<pmData.minValidPhredScore: badHeadStopIndex += 1 elif phredScore>=pmData.minValidPhredScore: foundBadHeadStop = True if foundBadTailStart is False: #check starts from the tail phredScore = smooth_phred_score_ls[-(i+1)] if phredScore<pmData.minValidPhredScore: badTailStart -= 1 elif phredScore>=pmData.minValidPhredScore: foundBadTailStart = True filtered_read_length = badTailStart-badHeadStopIndex-1 returnData = None if filtered_read_length>=pmData.minFinalReadLength: filtered_old_base_string = base_string[badHeadStopIndex+1:badTailStart] filtered_base_string = '' filtered_quality_string = quality_string[badHeadStopIndex+1:badTailStart] filtered_phred_score_ls = phred_score_ls[badHeadStopIndex+1:badTailStart] no_of_Ns = 0. for i in range(filtered_read_length): if filtered_phred_score_ls[i]<pmData.minValidPhredScore: filtered_base_string += 'N' no_of_Ns += 1 else: filtered_base_string += filtered_old_base_string[i] N_percentage = no_of_Ns/filtered_read_length if N_percentage<=pmData.maxNPercentage: returnData=PassingData(base_string=filtered_base_string, quality_string=filtered_quality_string) return returnData
