def phylogenetic_diversity_clade(self, options): """Calculate phylogenetic diversity of named groups.""" check_file_exists(options.decorated_tree) pd = PhylogeneticDiversity() pd.pd_clade(options.decorated_tree, options.output_file, options.taxa_list, options.rep_list)
def phylogenetic_diversity(self, options): """Calculate phylogenetic diversity of extant taxa.""" check_file_exists(options.tree) check_file_exists(options.taxa_list) pd = PhylogeneticDiversity() rtn = pd.pd(options.tree, options.taxa_list, options.per_taxa_pg_file) total_pd, num_in_taxa, in_pd, num_out_taxa, out_pd = rtn total_taxa = num_in_taxa + num_out_taxa in_pg = total_pd - out_pd # report phylogenetic diversity (PD) and gain (PG) print('') print('\tNo. Taxa\tPD\tPercent PD') print('%s\t%d\t%.2f\t%.2f%%' % ('Full tree', total_taxa, total_pd, 100)) print('%s\t%d\t%.2f\t%.3f%%' % ('Outgroup taxa (PD)', num_out_taxa, out_pd, out_pd * 100 / total_pd)) print('%s\t%d\t%.2f\t%.3f%%' % ('Ingroup taxa (PD)', num_in_taxa, in_pd, (in_pd) * 100 / total_pd)) print( '%s\t%d\t%.2f\t%.3f%%' % ('Ingroup taxa (PG)', num_in_taxa, in_pg, in_pg * 100 / total_pd))
def phylogenetic_diversity_clade(self, options): """Calculate phylogenetic diversity of named groups.""" check_file_exists(options.decorated_tree) pd = PhylogeneticDiversity() pd.pd_clade(options.decorated_tree, options.taxa_list, options.output_file)
def phylogenetic_diversity(self, options): """Calculate phylogenetic diversity of extant taxa.""" check_file_exists(options.tree) check_file_exists(options.taxa_list) pd = PhylogeneticDiversity() rtn = pd.pd(options.tree, options.taxa_list, options.rep_list, options.per_taxa_pg_file) total_pd, in_taxa, in_taxa_derep, in_pd, out_taxa, out_taxa_derep, out_pd = rtn total_taxa = in_taxa + out_taxa total_taxa_derep = in_taxa_derep + out_taxa_derep in_pg = total_pd - out_pd # report phylogenetic diversity (PD) and gain (PG) print '' print '\tNo. Taxa\tNo. Dereplicated Taxa\tPD\tPercent PD' print '%s\t%d\t%d\t%.2f\t%.2f%%' % ('Full tree', total_taxa, total_taxa_derep, total_pd, 100) print '%s\t%d\t%d\t%.2f\t%.3f%%' % ('Outgroup taxa (PD)', out_taxa, out_taxa_derep, out_pd, out_pd * 100 / total_pd) print '%s\t%d\t%d\t%.2f\t%.3f%%' % ('Ingroup taxa (PD)', in_taxa, in_taxa_derep, in_pd, (in_pd) * 100 / total_pd) print '%s\t%d\t%d\t%.2f\t%.3f%%' % ('Ingroup taxa (PG)', in_taxa, in_taxa_derep, in_pg, in_pg * 100 / total_pd)