def process_setup(self, inputFile, processName, suffix=None, suffixList=None):
"""
Return a tuple containing the output file and a boolean flag describing
whether the output file already exists
"""
log.info('Preparing to run %s on "%s"' % (processName, inputFile))
self.processCount += 1
if suffix:
outputFile = get_output_name(inputFile, suffix)
return outputFile
elif suffixList:
outputFiles = []
for suffix in suffixList:
outputFile = get_output_name( inputFile, suffix )
outputFiles.append( outputFile )
return outputFiles
def extract_ccs(input_file, output_file=None, min_length=LENGTH, min_snr=SNR):
"""
Extract CCS reads from an input_file
"""
output_file = output_file or get_output_name(input_file, 'fastq')
collection = BasH5Collection(input_file)
extract_ccs_fastq(collection, output_file, min_length, min_snr)
return output_file
def extract_ccs( input_file, output_file=None,
min_length=LENGTH,
min_snr=SNR):
"""
Extract CCS reads from an input_file
"""
output_file = output_file or get_output_name( input_file, 'fastq' )
collection = BasH5Collection( input_file )
extract_ccs_fastq( collection, output_file, min_length, min_snr )
return output_file
def process_setup(self,
inputFile,
processName,
suffix=None,
suffixList=None):
"""
Return a tuple containing the output file and a boolean flag describing
whether the output file already exists
"""
log.info('Preparing to run %s on "%s"' % (processName, inputFile))
self.processCount += 1
if suffix:
outputFile = get_output_name(inputFile, suffix)
return outputFile
elif suffixList:
outputFiles = []
for suffix in suffixList:
outputFile = get_output_name(inputFile, suffix)
outputFiles.append(outputFile)
return outputFiles
