"""Tool for creating PAM statistics."""
import argparse
import json
from lmpy.matrix import Matrix
from lmpy.tree import TreeWrapper
from lmpy.statistics.pam_stats import PamStats
DESCRIPTION = 'Compute statistics for a PAM and optionally a tree.'
# .....................................................................................
[docs]def cli():
"""Provide a command-line tool for computing statistics."""
parser = argparse.ArgumentParser(description=DESCRIPTION)
parser.add_argument('--tree_filename', type=str, help='Path to matching tree.')
parser.add_argument(
'--tree_matrix', type=str, nargs=3, help='Path to tree matrix.'
)
# Output matrices
parser.add_argument(
'--covariance_matrix',
type=str,
help='Path to write covariance matrix if desired.',
)
parser.add_argument(
'--diversity_matrix',
type=str,
help='Path to write diversity matrix if desired.',
)
parser.add_argument(
'--site_stats_matrix',
type=str,
help='Path to write site statistics matrix if desired.',
)
parser.add_argument(
'--species_stats_matrix',
type=str,
help='Path to write species statistics matrix if desired.',
)
# PAM
parser.add_argument('pam_filename', type=str, help='Path to PAM file.')
args = parser.parse_args()
tree = tree_matrix = node_heights_matrix = tip_lengths_matrix = None
pam = Matrix.load(args.pam_filename)
if args.tree_filename is not None:
tree = TreeWrapper.from_filename(args.tree_filename)
if args.tree_matrix is not None:
tree_matrix = Matrix.load(args.tree_matrix[0])
node_heights_matrix = Matrix.load(args.tree_matrix[1])
tip_lengths_matrix = Matrix.load(args.tree_matrix[2])
stats = PamStats(
pam,
tree=tree,
tree_matrix=tree_matrix,
node_heights_matrix=node_heights_matrix,
tip_lengths_matrix=tip_lengths_matrix,
)
# Write requested stats
if args.covariance_matrix is not None:
with open(args.covariance_matrix, mode='wt') as out_json:
json.dump(stats.calculate_covariance_statistics(), out_json)
if args.diversity_matrix is not None:
stats.calculate_diversity_statistics().write(args.diversity_matrix)
if args.site_stats_matrix is not None:
stats.calculate_site_statistics().write(args.site_stats_matrix)
if args.species_stats_matrix is not None:
stats.calculate_species_statistics().write(args.species_stats_matrix)
# .....................................................................................
__all__ = ['cli']
# .....................................................................................
if __name__ == '__main__': # pragma: no cover
cli()