INNER CODE UNIT · Python

__init__

hahnlab/CAFE5 · scripts/barista.py:9

    def __init__(self, config_file):
        self.command_line = list()
        self.config = ConfigParser.SafeConfigParser()
        self.config.read(config_file)

        self.binary_path = self.config.get('CAFExp folder', 'cafexp')

        # input files
        self.tree_path = self.config.get('input files', 'tree') # -t
        self.gene_families_path = self.config.get('input files', 'gene families', None) # -i
        self.lambda_tree_path = self.config.get('input files', 'lambda tree', None) # -y
        self.root_dist_path = self.config.get('input files', 'root distribution', None) # -f

        # options
        self.simulate = self.config.getboolean('options', 'simulate') # -s
        self.simulationsN = self.config.get('options', 'simulationsN', 0) # -n
        self.gammacatN = self.config.get('options', 'gammacatN', 1) # -k

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