def outliers(self, options):
"""Create information for identifying taxnomic outliers"""
check_file_exists(options.input_tree)
if options.plot_taxa_file:
check_file_exists(options.plot_taxa_file)
if options.trusted_taxa_file:
check_file_exists(options.trusted_taxa_file)
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
o = Outliers(options.dpi)
o.run(options.input_tree,
options.taxonomy_file,
options.output_dir,
options.plot_taxa_file,
options.plot_dist_taxa_only,
options.plot_domain,
options.trusted_taxa_file,
options.fixed_root,
options.min_children,
options.min_support,
options.verbose_table)
self.logger.info('Done.')
def outliers(self, options):
"""Create information for identifying taxnomic outliers"""
check_file_exists(options.input_tree)
check_file_exists(options.taxonomy_file)
if options.plot_taxa_file:
check_file_exists(options.plot_taxa_file)
if options.trusted_taxa_file:
check_file_exists(options.trusted_taxa_file)
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
if options.highlight_polyphyly and not options.fmeasure_table:
self.logger.error(
"The '--highlight_polyphyly' flag must be used with the '--fmeasure_table' flag."
)
return
o = Outliers(options.skip_mpld3, options.dpi, options.output_dir)
o.run(options.input_tree, options.taxonomy_file, options.viral,
options.plot_taxa_file, options.plot_dist_taxa_only,
options.plot_domain, options.highlight_polyphyly,
options.highlight_taxa_file, options.trusted_taxa_file,
options.fixed_root, options.min_children, options.min_support,
options.mblet, options.fmeasure_table, options.min_fmeasure,
options.fmeasure_mono, options.verbose_table)
self.logger.info('Done.')
def outliers(self, options):
"""Create information for identifying taxnomic outliers"""
check_file_exists(options.input_tree)
if options.plot_taxa_file:
check_file_exists(options.plot_taxa_file)
if options.trusted_taxa_file:
check_file_exists(options.trusted_taxa_file)
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
o = Outliers(options.dpi)
o.run(options.input_tree, options.taxonomy_file, options.output_dir,
options.plot_taxa_file, options.plot_dist_taxa_only,
options.plot_domain, options.trusted_taxa_file,
options.fixed_root, options.min_children, options.min_support,
options.verbose_table)
self.logger.info('Done.')
