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)