CoverView.py 文件源码

def __init__(self, threadidx, options, config, startline, endline, names):
        multiprocessing.Process.__init__(self)

        # Initializing variables
        self.threadidx = threadidx
        self.options = options
        self.config = config
        self.startline = startline
        self.endline = endline
        self.names = names

        # Initializing reads directory
        self.reads = dict()

        # Connecting to BAM file
        self.samfile = pysam.Samfile(options.input, "rb")

        # Connecting to transcript database file
        if not config['transcript_db'] is None:
            self.enstdb = pysam.Tabixfile(config['transcript_db'])
        else:
            self.enstdb = None

        # Initializing output files
        if int(options.threads) > 1:
            if config['outputs']['regions']:
                self.out_targets = open(options.output + '_regions_tmp_' + str(threadidx) + '.txt', 'w')
            if config['outputs']['profiles']:
                self.out_profiles = open(options.output + '_profiles_tmp_' + str(threadidx) + '.txt', 'w')
                if not config['transcript_db'] is None:
                    self.out_poor = open(options.output + '_poor_tmp_' + str(threadidx) + '.txt', 'w')
        else:
            if config['outputs']['regions']:
                self.out_targets = open(options.output + '_regions.txt', 'w')
            if config['outputs']['profiles']:
                self.out_profiles = open(options.output + '_profiles.txt', 'w')
                if not config['transcript_db'] is None:
                    self.out_poor = open(options.output + '_poor.txt', 'w')

    # Checking if target is fail or pass