def compute_mean_densities(self):
codon_counts = self.read_file('buffered_codon_counts', merged=True)
mean_densities = positions.compute_averaged_codon_densities(codon_counts)
self.write_file('mean_densities', mean_densities)
mean_densities_anisomycin = positions.compute_averaged_codon_densities(codon_counts, offset_key='anisomycin')
self.write_file('mean_densities_anisomycin', mean_densities_anisomycin)
if self.possibly_misannotated_file_name != None:
possibly_misannotated_names = {line.strip() for line in open(self.possibly_misannotated_file_name)}
mean_densities = positions.compute_averaged_codon_densities(codon_counts, possibly_misannotated_names)
self.write_file('mean_densities_no_misannotated', mean_densities)
def compute_mean_densities(self):
codon_counts = self.read_file('simulated_codon_counts')
mean_densities = positions.compute_averaged_codon_densities(codon_counts)
self.write_file('mean_densities', mean_densities)