def codon_usage(self, options):
"""Codon usage command"""
self.logger.info('')
self.logger.info('*******************************************************************************')
self.logger.info(' [CompareM - codon_usage] Calculating codon usage within each genome.')
self.logger.info('*******************************************************************************')
self.logger.info('')
check_dir_exists(options.gene_dir)
# get list of files with called genes
gene_files = []
files = os.listdir(options.gene_dir)
for f in files:
if f.endswith(options.gene_ext):
gene_files.append(os.path.join(options.gene_dir, f))
# warn use if no files were found
if len(gene_files) == 0:
self.logger.warning(' [Warning] No gene files found. Check the --gene_ext flag used to identify gene files.')
return
# calculate amino acid usage
codon_usage = CodonUsage(options.cpus, options.keep_ambiguous)
genome_codon_usage, codon_set, _mean_length = codon_usage.run(gene_files)
# write out results
self._write_usage_profile(genome_codon_usage, codon_set, options.output_file)
self.logger.info('')
self.logger.info(' Codon usage written to: %s' % options.output_file)
self.time_keeper.print_time_stamp()
def stop_usage(self, options):
"""Stop codon usage command"""
gene_files = self._input_files(options.nucleotide_gene_files, options.file_ext)
# calculate amino acid usage
codon_usage = CodonUsage(options.cpus, keep_ambiguous=False, stop_codon_only=True)
genome_codon_usage, codon_set, mean_gene_length = codon_usage.run(gene_files)
# write out results
if not options.mean_gene_length:
self._write_usage_profile(genome_codon_usage, codon_set, options.counts, options.output_file)
else:
fout = open(options.output_file, 'w')
for codon in codon_set:
fout.write('\t' + codon)
if mean_gene_length:
fout.write('\t' + codon + ': avg. seq. length')
fout.write('\n')
for genome_id, codons in genome_codon_usage.items():
fout.write(genome_id)
for codon in codon_set:
fout.write('\t%d' % codons.get(codon, 0))
if mean_gene_length:
mean_len = mean_gene_length[genome_id].get(codon, None)
if mean_len:
fout.write('\t%.1f' % mean_len)
else:
fout.write('\tna')
fout.write('\n')
self.logger.info('Stop codon usage written to: %s' % options.output_file)
def stop_usage(self, options):
"""Stop codon usage command"""
self.logger.info('')
self.logger.info('*******************************************************************************')
self.logger.info(' [CompareM - stop_usage] Calculating stop codon usage within each genome.')
self.logger.info('*******************************************************************************')
self.logger.info('')
check_dir_exists(options.gene_dir)
# get list of files with called genes
gene_files = []
files = os.listdir(options.gene_dir)
for f in files:
if f.endswith(options.gene_ext):
gene_files.append(os.path.join(options.gene_dir, f))
# warn use if no files were found
if len(gene_files) == 0:
self.logger.warning(' [Warning] No gene files found. Check the --gene_ext flag used to identify gene files.')
return
# calculate amino acid usage
codon_usage = CodonUsage(options.cpus, keep_ambiguous=False, stop_codon_only=True)
genome_codon_usage, codon_set, mean_gene_length = codon_usage.run(gene_files)
# write out results
fout = open(options.output_file, 'w')
for codon in codon_set:
fout.write('\t' + codon)
if mean_gene_length:
fout.write('\t' + codon + ': avg. seq. length')
fout.write('\n')
for genome_id, codons in genome_codon_usage.iteritems():
fout.write(genome_id)
for codon in codon_set:
fout.write('\t%d' % codons.get(codon, 0))
if mean_gene_length:
mean_len = mean_gene_length[genome_id].get(codon, None)
if mean_len:
fout.write('\t%.1f' % mean_len)
else:
fout.write('\tna')
fout.write('\n')
self.logger.info('')
self.logger.info(' Stop codon usage written to: %s' % options.output_file)
self.time_keeper.print_time_stamp()
def codon_usage(self, options):
"""Codon usage command"""
gene_files = self._input_files(options.nucleotide_gene_files, options.file_ext)
# calculate amino acid usage
codon_usage = CodonUsage(options.cpus, options.keep_ambiguous)
genome_codon_usage, codon_set, _mean_length = codon_usage.run(gene_files)
# write out results
self._write_usage_profile(genome_codon_usage, codon_set, options.counts, options.output_file)
self.logger.info('Codon usage written to: %s' % options.output_file)
def codon_usage(self, options):
"""Codon usage command"""
gene_files = self._input_files(options.nucleotide_gene_files,
options.file_ext)
# calculate amino acid usage
codon_usage = CodonUsage(options.cpus, options.keep_ambiguous)
genome_codon_usage, codon_set, _mean_length = codon_usage.run(
gene_files)
# write out results
self._write_usage_profile(genome_codon_usage, codon_set,
options.counts, options.output_file)
self.logger.info('Codon usage written to: %s' % options.output_file)
def stop_usage(self, options):
"""Stop codon usage command"""
gene_files = self._input_files(options.nucleotide_gene_files,
options.file_ext)
# calculate amino acid usage
codon_usage = CodonUsage(options.cpus,
keep_ambiguous=False,
stop_codon_only=True)
genome_codon_usage, codon_set, mean_gene_length = codon_usage.run(
gene_files)
# write out results
if not options.mean_gene_length:
self._write_usage_profile(genome_codon_usage, codon_set,
options.counts, options.output_file)
else:
fout = open(options.output_file, 'w')
for codon in codon_set:
fout.write('\t' + codon)
if mean_gene_length:
fout.write('\t' + codon + ': avg. seq. length')
fout.write('\n')
for genome_id, codons in genome_codon_usage.items():
fout.write(genome_id)
for codon in codon_set:
fout.write('\t%d' % codons.get(codon, 0))
if mean_gene_length:
mean_len = mean_gene_length[genome_id].get(codon, None)
if mean_len:
fout.write('\t%.1f' % mean_len)
else:
fout.write('\tna')
fout.write('\n')
self.logger.info('Stop codon usage written to: %s' %
options.output_file)
