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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.
##
##############################################################################
"""
Tests for PHYLIP tree list writing.
"""
import unittest
import dendropy
from dendropy.test.support import dendropytest
from dendropy.test.support import compare_and_validate
from dendropy.test.support import pathmap
from dendropy.test.support import standard_file_test_chars
class PhylipWriterCharactersTestCase(
compare_and_validate.ValidateWriteable,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.check_taxon_annotations = False
cls.check_matrix_annotations = False
cls.check_sequence_annotations = False
cls.check_column_annotations = False
cls.check_cell_annotations = False
standard_file_test_chars.DnaTestChecker.build()
standard_file_test_chars.RnaTestChecker.build()
standard_file_test_chars.ProteinTestChecker.build()
standard_file_test_chars.Standard01234TestChecker.build()
standard_file_test_chars.ContinuousTestChecker.build()
cls.srcs = (
("standard-test-chars-dna.relaxed.phylip", dendropy.DnaCharacterMatrix, standard_file_test_chars.DnaTestChecker),
("standard-test-chars-rna.relaxed.phylip", dendropy.RnaCharacterMatrix, standard_file_test_chars.RnaTestChecker),
("standard-test-chars-protein.relaxed.phylip", dendropy.ProteinCharacterMatrix, standard_file_test_chars.ProteinTestChecker),
("standard-test-chars-generic.relaxed.phylip", dendropy.StandardCharacterMatrix, standard_file_test_chars.Standard01234TestChecker),
("standard-test-chars-continuous.relaxed.phylip", dendropy.ContinuousCharacterMatrix, standard_file_test_chars.ContinuousTestChecker),
)
def verify_char_matrix(self, char_matrix, src_matrix_checker_type):
self.assertEqual(type(char_matrix), src_matrix_checker_type.matrix_type)
if src_matrix_checker_type.matrix_type is dendropy.StandardCharacterMatrix:
src_matrix_checker_type.create_class_fixtures_label_sequence_map_based_on_state_alphabet(src_matrix_checker_type,
char_matrix.default_state_alphabet)
standard_file_test_chars.general_char_matrix_checker(
self,
char_matrix,
src_matrix_checker_type,
check_taxon_annotations=self.check_taxon_annotations,
check_matrix_annotations=self.check_matrix_annotations,
check_sequence_annotations=self.check_sequence_annotations,
check_column_annotations=self.check_column_annotations,
check_cell_annotations=self.check_cell_annotations,)
def test_basic_phylip_chars(self):
for src_filename, matrix_type, src_matrix_checker_type in self.__class__.srcs:
src_path = pathmap.char_source_path(src_filename)
d1 = matrix_type.get_from_path(src_path, "phylip")
for strict in (True, False):
for spaces_to_underscores in (True, False):
for force_unique_taxon_labels in (True, False):
s = self.write_out_validate_equal_and_return(
d1, "phylip", {
"strict": strict,
"spaces_to_underscores" : spaces_to_underscores,
"force_unique_taxon_labels" : force_unique_taxon_labels,
})
d2 = matrix_type.get_from_string(s, "phylip")
self.verify_char_matrix(d2, src_matrix_checker_type)
class PhylipWriterCharactersVariantsTestCase(dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
d = dendropy.DnaCharacterMatrix()
cls.original_labels = [
"a0_123456789_1",
"a0_123456789_2",
"a0_123456789_3",
"a0_123456789_4",
"a0_123456789_5",
"b0_123456789_1",
"b0_123456789_2",
"b0_123456789_3",
"b0_123456789_4",
]
for label in cls.original_labels:
t = d.taxon_namespace.require_taxon(label=label)
d[t] = d.default_state_alphabet.get_states_for_symbols("AACGT")
cls.data = d
def test_strict_write(self):
s0 = self.data.as_string("phylip", strict=True)
d2 = dendropy.DnaCharacterMatrix.get_from_string(s0, "phylip", strict=True)
obs_labels = set([t.label for t in d2])
self.assertEqual(len(obs_labels), len(self.original_labels))
for t in d2:
self.assertEqual(len(t.label), 10)
self.assertEqual(d2[t].symbols_as_string(), "AACGT")
if __name__ == "__main__":
unittest.main()
|
