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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
import collections
import sys
if not (sys.version_info.major >= 3 and sys.version_info.minor >= 4):
from dendropy.utility.filesys import pre_py34_open as open
from dendropy.test.support import pathmap
_SPLITS_REFERENCE_FIELD_TYPES = [str, int, int, float, float]
def get_splits_reference(
splits_filename,
splits_dir=None,
key_column_index=0):
# Key columns are:
# 0 : PAUP* bipartition string representation '....**...' etc.
# 1 : unnormalized split bitmask (for rooted trees) == leafset_bitmask for all trees and split_bitmask for rooted trees
# 2 : normalized split bitmask (for unrooted trees) == split_bitmask for unrooted trees
# 3 : (weighted) counts
# 4 : (weighted) frequencies
if splits_dir is not None:
splits_filepath = os.path.join(splits_dir, splits_filename)
else:
splits_filepath = pathmap.splits_source_path(splits_filename)
d = collections.OrderedDict()
with open(splits_filepath, "r") as src:
for row in src:
content = row.split("#")[0]
if not content:
continue
fields = content.split("\t")
assert len(fields) == 5, "{}: {}".format(content, fields)
for idx, field in enumerate(fields):
fields[idx] = _SPLITS_REFERENCE_FIELD_TYPES[idx](fields[idx])
key = fields[key_column_index]
d[key] = {
"bipartition_string": fields[0],
"unnormalized_split_bitmask": fields[1],
"normalized_split_bitmask": fields[2],
"count": fields[3],
"frequency": fields[4]/100,
}
return d
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