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