def process_assembled(myData):
# take each read contig (from PEAR alignment) and search for the expected
# linker sequence. If we find it, extract the r1 and r2 and process
# into separate files. Takes of reverse complement of r1, and imposes
# min score on linker alignment. Tests if reads are longer than 22 bp. If not, they are
# written in the lenFail fastq files
myData['newR1FileName'] = myData['outDir'] + myData['sampleName'] + '.processed.R1.fq.gz'
myData['newR2FileName'] = myData['outDir'] + myData['sampleName'] + '.processed.R2.fq.gz'
outR1 = genutils.open_gzip_write(myData['newR1FileName'])
outR2 = genutils.open_gzip_write(myData['newR2FileName'])
myData['lenFail_R1FileName'] = myData['outDir'] + myData['sampleName'] + '.lenFail.R1.fq.gz'
myData['lenFail_R2FileName'] = myData['outDir'] + myData['sampleName'] + '.lenFail.R2.fq.gz'
lenFailR1 = genutils.open_gzip_write(myData['lenFail_R1FileName'])
lenFailR2 = genutils.open_gzip_write(myData['lenFail_R2FileName'])
myData['numAssembled'] = 0
myData['numOK'] = 0
myData['numFail'] = 0
myData['lenFail'] = 0
fqFile = genutils.open_gzip_read(myData['assembledFQ'])
while True:
R1 = fastqstats.get_next_seq_record(fqFile)
if R1 is None: break
myData['numAssembled'] += 1
res = check_seq(R1,myData)
if res['passChecks'] is True:
passLength = read_len_test(res)
if passLength is True:
myData['numOK'] += 1
name = R1['readName']
name = name.split()[0]
name1 = name + ' 1'
name2 = name + ' 2'
outR1.write('@%s\n%s\n+\n%s\n' % (name1,res['seq1'],res['seq1Qual']))
outR2.write('@%s\n%s\n+\n%s\n' % (name2,res['seq2'],res['seq2Qual']))
else:
myData['numFail'] += 1
if myData['numAssembled'] % 25000 == 0:
print '\tProcesssed %i assembled seqs...' % (myData['numAssembled'])
if res['passChecks'] is True and passLength is False:
myData['lenFail'] += 1
name = R1['readName']
name = name.split()[0]
name1 = name + ' 1'
name2 = name + ' 2'
lenFailR1.write('@%s\n%s\n+\n%s\n' % (name1,res['seq1'],res['seq1Qual']))
lenFailR2.write('@%s\n%s\n+\n%s\n' % (name2,res['seq2'],res['seq2Qual']))
# if myData['numAssembled'] >= 1000:
# break
fqFile.close()
myData['totReads'] = myData['numAssembled'] + myData['numDiscarded'] + myData['numNotAssem']
outR1.close()
outR2.close()
def count_num_discarded(myData):
myData['numDiscarded'] = 0
fqFile = genutils.open_gzip_read(myData['discardedFQ'])
while True:
R1 = fastqstats.get_next_seq_record(fqFile)
if R1 is None: break
myData['numDiscarded'] += 1
fqFile.close()
def count_num_not_assembled(myData):
myData['numNotAssem'] = 0
fqFile = genutils.open_gzip_read(myData['notAssemF'])
while True:
R1 = fastqstats.get_next_seq_record(fqFile)
if R1 is None: break
myData['numNotAssem'] += 1
fqFile.close()
