def bl_table(self, options):
"""Produce table with number of lineage for increasing mean branch lengths."""
check_file_exists(options.input_tree)
check_file_exists(options.taxon_category)
b = BranchLengthDistribution()
b.table(options.input_tree, options.taxon_category, options.step_size,
options.output_table)
self.logger.info('Done.')
def bl_dist(self, options):
"""Calculate distribution of branch lengths at each taxonomic rank."""
check_file_exists(options.input_tree)
make_sure_path_exists(options.output_dir)
b = BranchLengthDistribution()
b.run(options.input_tree, options.trusted_taxa_file,
options.min_children, options.taxonomy_file, options.output_dir)
self.logger.info('Done.')
def bl_decorate(self, options):
"""Decorate tree based using a mean branch length criterion."""
check_file_exists(options.input_tree)
b = BranchLengthDistribution()
b.decorate(options.input_tree, options.taxonomy_file,
options.threshold, options.rank,
options.retain_named_lineages, options.keep_labels,
options.prune, options.output_tree)
self.logger.info('Done.')
def bl_table(self, options):
"""Produce table with number of lineage for increasing mean branch lengths."""
check_file_exists(options.input_tree)
check_file_exists(options.taxon_category)
b = BranchLengthDistribution()
b.table(options.input_tree,
options.taxon_category,
options.step_size,
options.output_table)
self.logger.info('Done.')
def bl_optimal(self, options):
"""Determine branch length for best congruency with existing taxonomy."""
b = BranchLengthDistribution()
optimal_bl, correct_taxa, incorrect_taxa = b.optimal(
options.input_tree, options.rank, options.min_dist,
options.max_dist, options.step_size, options.output_table)
prec = float(correct_taxa) / (correct_taxa + incorrect_taxa)
self.logger.info('Optimal branch length is %f.' % optimal_bl)
self.logger.info(
'This results in %d correct and %d incorrect taxa (precision = %.2f).'
% (correct_taxa, incorrect_taxa, prec))
def bl_dist(self, options):
"""Calculate distribution of branch lengths at each taxonomic rank."""
check_file_exists(options.input_tree)
make_sure_path_exists(options.output_dir)
b = BranchLengthDistribution()
b.run(options.input_tree,
options.trusted_taxa_file,
options.min_children,
options.taxonomy_file,
options.output_dir)
self.logger.info('Done.')
def bl_optimal(self, options):
"""Determine branch length for best congruency with existing taxonomy."""
b = BranchLengthDistribution()
optimal_bl, correct_taxa, incorrect_taxa = b.optimal(options.input_tree,
options.rank,
options.min_dist,
options.max_dist,
options.step_size,
options.output_table)
prec = float(correct_taxa) / (correct_taxa + incorrect_taxa)
self.logger.info('Optimal branch length is %f.' % optimal_bl)
self.logger.info('This results in %d correct and %d incorrect taxa (precision = %.2f).' % (correct_taxa, incorrect_taxa, prec))
def bl_decorate(self, options):
"""Decorate tree based using a mean branch length criterion."""
check_file_exists(options.input_tree)
b = BranchLengthDistribution()
b.decorate(options.input_tree,
options.taxonomy_file,
options.threshold,
options.rank,
options.retain_named_lineages,
options.keep_labels,
options.prune,
options.output_tree)
self.logger.info('Done.')
