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def kmer_usage(self, options):
"""Kmer usage command"""
if options.k > 10 or options.k <= 0:
self.logger.warning('CompareM only support kmers with k <= 10.')
sys.exit(0)
genome_files = self._input_files(options.genome_files, options.file_ext)
# calculate amino acid usage
kmer_usage = KmerUsage(options.k, options.cpus)
genome_kmer_usage, kmer_set = kmer_usage.run(genome_files)
# write out results
self.logger.info('Writing kmer profiles to file (be patient!).')
self._write_usage_profile(genome_kmer_usage,
kmer_set,
options.counts,
options.output_file)
self.logger.info('Kmer usage written to: %s' % options.output_file)