def phred64to33(inputFq, outputFq):
'''convert phred64 scaling fastq file format to phred33.'''
from Bio import SeqIO
if inputFq.endswith('.gz'):
tmpIN = re.sub(r'.gz$', '', inputFq)
assert not os.system('gzip -cdf %s > %s' % (inputFq, tmpIN))
else:
tmpIN = inputFq
if outputFq.endswith('.gz'):
tmpOUT = re.sub(r'.gz$', '', outputFq)
SeqIO.covert(tmpIN, "fastq-illumina", tmpOUT, "fastq-sanger")
assert not os.system('gzip -f %s' % tmpOUT)
else:
SeqIO.covert(tmpIN, "fastq-illumina", outputFq, "fastq-sanger")
def phred64to33(inputFq, outputFq):
'''convert phred64 scaling fastq file format to phred33.'''
from Bio import SeqIO
if inputFq.endswith('.gz'):
tmpIN = re.sub(r'.gz$', '', inputFq)
assert not os.system('gzip -cdf %s > %s' % (inputFq, tmpIN))
else:
tmpIN = inputFq
if outputFq.endswith('.gz'):
tmpOUT = re.sub(r'.gz$', '', outputFq)
SeqIO.covert(tmpIN, "fastq-illumina", tmpOUT, "fastq-sanger")
assert not os.system('gzip -f %s' % tmpOUT)
else:
SeqIO.covert(tmpIN, "fastq-illumina", outputFq, "fastq-sanger")
