INNER CODE UNIT · Python

build_command_line

hahnlab/CAFE5 · scripts/barista.py:48

    def build_command_line(self):
        self.command_line.append(os.path.join(self.binary_path, 'cafexp'))

        self.add_option('-l', self.a_lambda)
        self.add_option('-p', self.a_poisson_lambda)
        self.add_option('-t', self.tree_path)
        self.add_option('-n', self.simulationsN)
        self.add_option('-f', self.root_dist_path)
        self.add_option('-k', self.gammacatN)
        self.add_option('-i', self.gene_families_path)
        self.add_option('-o', self.output_suffix)
        
        if self.simulate:
            self.command_line += ['-s']
        
    def pour_me_one(self):
        print " ".join(self.command_line)
        return subprocess.check_output(" ".join(self.command_line), shell=True)

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