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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 general NEXUS character matrix reading.
"""
import unittest
import dendropy
from dendropy.utility import error
from dendropy.test.support import dendropytest
from dendropy.test.support import pathmap
from dendropy.test.support import standard_file_test_chars
from dendropy.test.support import compare_and_validate
from dendropy.dataio import nexmlreader
from dendropy.utility import messaging
_LOG = messaging.get_logger(__name__)
class NexmlCharactersReaderDnaTestCase(
standard_file_test_chars.DnaTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_nexml(self):
src_filenames = [
"standard-test-chars-dna.as_cells.nexml",
"standard-test-chars-dna.as_seqs.nexml",
]
for src_idx, src_filename in enumerate(src_filenames):
# print(src_idx, src_filename)
src_path = pathmap.char_source_path(src_filename)
self.verify_get_from(
matrix_type=dendropy.DnaCharacterMatrix,
src_filepath=src_path,
schema="nexml",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class NexmlCharactersReaderRnaTestCase(
standard_file_test_chars.RnaTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_nexml(self):
src_filenames = [
"standard-test-chars-rna.as_cells.nexml",
"standard-test-chars-rna.as_seqs.nexml",
]
for src_idx, src_filename in enumerate(src_filenames):
# print(src_idx, src_filename)
src_path = pathmap.char_source_path(src_filename)
self.verify_get_from(
matrix_type=dendropy.RnaCharacterMatrix,
src_filepath=src_path,
schema="nexml",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class NexmlCharactersReaderProteinTestCase(
standard_file_test_chars.ProteinTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_nexml(self):
src_filenames = [
"standard-test-chars-protein.as_cells.nexml",
"standard-test-chars-protein.as_seqs.nexml",
]
for src_idx, src_filename in enumerate(src_filenames):
# print(src_idx, src_filename)
src_path = pathmap.char_source_path(src_filename)
self.verify_get_from(
matrix_type=dendropy.ProteinCharacterMatrix,
src_filepath=src_path,
schema="nexml",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class NexmlCharactersContinuousTestCase(
standard_file_test_chars.ContinuousTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_nexml(self):
src_filenames = [
"standard-test-chars-continuous.as_cells.nexml",
"standard-test-chars-continuous.as_seqs.nexml",
]
for src_idx, src_filename in enumerate(src_filenames):
# print(src_idx, src_filename)
src_path = pathmap.char_source_path(src_filename)
self.verify_get_from(
matrix_type=dendropy.ContinuousCharacterMatrix,
src_filepath=src_path,
schema="nexml",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class NexmlStandardCharacters01234TestCase(
standard_file_test_chars.Standard01234TestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_nexml(self):
src_filenames = [
"standard-test-chars-generic.as_cells.nexml",
"standard-test-chars-generic.as_seqs.nexml",
]
for src_idx, src_filename in enumerate(src_filenames):
# print(src_idx, src_filename)
src_path = pathmap.char_source_path(src_filename)
self.verify_get_from(
matrix_type=dendropy.StandardCharacterMatrix,
src_filepath=src_path,
schema="nexml",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
if __name__ == "__main__":
unittest.main()
|
