def binomial(self, options):
"""Ensure species are designated using binomial nomenclature."""
check_file_exists(options.input_taxonomy)
fout = open(options.output_taxonomy, 'w')
taxonomy = Taxonomy()
t = taxonomy.read(options.input_taxonomy)
for genome_id, taxon_list in t.items():
taxonomy_str = ';'.join(taxon_list)
if not taxonomy.check_full(taxonomy_str):
sys.exit(-1)
genus = taxon_list[5][3:]
species = taxon_list[6][3:]
if species and genus not in species:
taxon_list[6] = 's__' + genus + ' ' + species
taxonomy_str = ';'.join(taxon_list)
fout.write('%s\t%s\n' % (genome_id, taxonomy_str))
fout.close()
self.logger.info('Revised taxonomy written to: %s' %
options.output_taxonomy)
def fill_ranks(self, options):
"""Ensure taxonomy strings contain all 7 canonical ranks."""
check_file_exists(options.input_taxonomy)
fout = open(options.output_taxonomy, 'w')
taxonomy = Taxonomy()
t = taxonomy.read(options.input_taxonomy)
for genome_id, taxon_list in t.iteritems():
full_taxon_list = taxonomy.fill_missing_ranks(taxon_list)
taxonomy_str = ';'.join(full_taxon_list)
if not taxonomy.check_full(taxonomy_str):
sys.exit(-1)
fout.write('%s\t%s\n' % (genome_id, taxonomy_str))
fout.close()
self.logger.info('Revised taxonomy written to: %s' % options.output_taxonomy)
def fill_ranks(self, options):
"""Ensure taxonomy strings contain all 7 canonical ranks."""
check_file_exists(options.input_taxonomy)
fout = open(options.output_taxonomy, 'w')
taxonomy = Taxonomy()
t = taxonomy.read(options.input_taxonomy)
for genome_id, taxon_list in t.items():
full_taxon_list = taxonomy.fill_missing_ranks(taxon_list)
taxonomy_str = ';'.join(full_taxon_list)
if not taxonomy.check_full(taxonomy_str):
sys.exit(-1)
fout.write('%s\t%s\n' % (genome_id, taxonomy_str))
fout.close()
self.logger.info('Revised taxonomy written to: %s' % options.output_taxonomy)
