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def aa_usage(self, options):
"""Amino acid usage command"""
gene_files = self._input_files(options.protein_gene_files, options.file_ext)
# calculate amino acid usage
amino_acid_usage = AminoAcidUsage(options.cpus)
genome_aa_usage, aa_set = amino_acid_usage.run(gene_files)
# write out results
self._write_usage_profile(genome_aa_usage,
aa_set,
options.counts,
options.output_file)
self.logger.info('Amino acid usage written to: %s' % options.output_file)