def main():
"""Main method for script."""
parser = argparse.ArgumentParser()
parser.add_argument('shapegrid_filename',
type=str,
help='File location of the shapegrid shapefile')
parser.add_argument('pam_filename',
type=str,
help='File location of the PAM matrix for statistics')
parser.add_argument('tree_filename',
type=str,
help='File location of the tree to use for statistics')
parser.add_argument('tree_schema',
choices=['newick', 'nexus'],
help='The tree schema')
parser.add_argument('out_geojson_filename',
type=str,
help='File location to write the output GeoJSON')
parser.add_argument('--layer',
nargs=2,
action='append',
help='File location of a layer followed by a label')
args = parser.parse_args()
# Load data
pam = Matrix.load(args.pam_filename)
tree = TreeWrapper.get(path=args.tree_filename, schema=args.tree_schema)
# Encode layers
encoded_layers = encode_environment_layers(args.shapegrid_filename,
args.layer)
# Calculate PAM statistics
stats_mtx = calculate_tree_site_statistics(pam, tree)
# Join encoded layers and PAM statistics
mtx = join_encoded_layers_and_pam_stats(encoded_layers, stats_mtx)
# Generate GeoJSON
geojson_data = create_geojson(args.shapegrid_filename, mtx)
# Write GeoJSON
with open(args.out_geojson_filename, 'w') as out_file:
json.dump(geojson_data, out_file)
def main():
"""Main method for script."""
parser = argparse.ArgumentParser()
parser.add_argument('--out_stats_matrix_filename',
type=str,
help='Location to write statistics matrix.')
parser.add_argument('shapegrid_filename',
type=str,
help='File location of the shapegrid shapefile')
parser.add_argument('pam_filename',
type=str,
help='File location of the PAM matrix for statistics')
parser.add_argument('tree_filename',
type=str,
help='File location of the tree to use for statistics')
parser.add_argument('tree_schema',
choices=['newick', 'nexus'],
help='The tree schema')
parser.add_argument('out_geojson_filename',
type=str,
help='File location to write the output GeoJSON')
parser.add_argument('out_csv_filename',
type=str,
help='File location to write the output CSV')
parser.add_argument('out_matrix_filename',
type=str,
help='File location to write the output matrix')
parser.add_argument('--layer',
nargs=2,
action='append',
help='File location of a layer followed by a label')
args = parser.parse_args()
# Load data
pam = Matrix.load(args.pam_filename)
tree = TreeWrapper.get(path=args.tree_filename, schema=args.tree_schema)
# Encode layers
encoded_layers = encode_environment_layers(args.shapegrid_filename,
args.layer)
# Calculate PAM statistics
stats_mtx = calculate_tree_site_statistics(pam, tree)
if args.out_stats_matrix_filename:
stats_mtx.write(args.out_stats_matrix_filename)
# Join encoded layers and PAM statistics
mtx = join_encoded_layers_and_pam_stats(encoded_layers, stats_mtx)
# Generate GeoJSON
geojson_data = create_geojson(args.shapegrid_filename, mtx)
# Write GeoJSON
with open(args.out_geojson_filename, 'w') as out_file:
json.dump(geojson_data, out_file, indent=4)
# Write matrix data
new_rh = []
res = 0.5
for _, x, y in mtx.get_row_headers():
min_x = x - res
max_x = x + res
min_y = y - res
max_y = y + res
new_rh.append('"POLYGON (({} {},{} {},{} {},{} {},{} {}))"'.format(
min_x, max_y, max_x, max_y, max_x, min_y, min_x, min_y, min_x,
max_y))
mtx.write(args.out_matrix_filename)
mtx.set_row_headers(new_rh)
with open(args.out_csv_filename, 'w') as out_file:
mtx.write_csv(out_file)
