KmcFastq.py 文件源码

def __init__(self,output_directory, input_filename, threads, kmer, min_kmers_threshold, max_kmers_threshold, verbose):
        self.logger = logging.getLogger(__name__)
        self.output_directory = output_directory
        self.input_filename = input_filename
        self.threads = threads
        self.kmer = kmer

        if self.file_type_option() == '-fm':
            # a FASTA file doesnt have a depth of coverage
            self.min_kmers_threshold = 1
        else:
            self.min_kmers_threshold = min_kmers_threshold

        self.max_kmers_threshold = max_kmers_threshold
        self.temp_working_dir = tempfile.mkdtemp(dir=os.path.abspath(output_directory),prefix='tmp_samplekmers_')
        self.verbose = verbose
        if self.verbose:
            self.logger.setLevel(logging.DEBUG)
        else:
            self.logger.setLevel(logging.ERROR)