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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 PHYLIP character matrix reading.
"""
import unittest
import dendropy
import collections
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 phylipreader
from dendropy.utility import messaging
_LOG = messaging.get_logger(__name__)
class PhylipCharactersReaderDnaTestCase(
standard_file_test_chars.DnaTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_phylip(self):
src_filenames = [
"standard-test-chars-dna.relaxed.phylip",
]
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="phylip",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class PhylipCharactersReaderRnaTestCase(
standard_file_test_chars.RnaTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_phylip(self):
src_filenames = [
"standard-test-chars-rna.relaxed.phylip",
]
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="phylip",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class PhylipCharactersReaderProteinTestCase(
standard_file_test_chars.ProteinTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_phylip(self):
src_filenames = [
"standard-test-chars-protein.relaxed.phylip",
]
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="phylip",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class PhylipStandardCharacters01234TestCase(
standard_file_test_chars.Standard01234TestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build(state_alphabet_fundamental_symbols="0123456789-")
def test_basic_phylip(self):
src_filenames = [
"standard-test-chars-generic.relaxed.phylip",
]
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="phylip",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class PhylipCharactersContinuousTestCase(
standard_file_test_chars.ContinuousTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_nexus(self):
src_filenames = [
("standard-test-chars-continuous.relaxed.phylip", {}),
("standard-test-chars-continuous.interleaved.phylip", {"interleaved": True}),
]
for src_idx, (src_filename, kwargs) 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="phylip",
factory_kwargs=kwargs,
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class PhylipVariantsTestCases(dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.expected_seqs = collections.OrderedDict()
cls.expected_seqs["Turkey"] = "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT"
cls.expected_seqs["Salmo gair"] = "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT"
cls.expected_seqs["H. Sapiens"] = "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA"
cls.expected_seqs["Chimp"] = "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT"
cls.expected_seqs["Gorilla"] = "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA"
def test_strict_sequential(self):
s = """\
5 42
Turkey AAGCTNGGGC ATTTCAGGGT
GAGCCCGGGC AATACAGGGT AT
Salmo gairAAGCCTTGGC AGTGCAGGGT
GAGCCGTGGC CGGGCACGGT AT
H. SapiensACCGGTTGGC CGTTCAGGGT
ACAGGTTGGC CGTTCAGGGT AA
Chimp AAACCCTTGC CGTTACGCTT
AAACCGAGGC CGGGACACTC AT
Gorilla AAACCCTTGC CGGTACGCTT
AAACCATTGC CGGTACGCTT AA
"""
char_matrix = dendropy.DnaCharacterMatrix.get_from_string(
s,
"phylip",
strict=True)
self.assertEqual(len(char_matrix), len(self.expected_seqs))
self.assertEqual(len(char_matrix.taxon_namespace), len(self.expected_seqs))
for taxon, expected_taxon in zip(char_matrix, self.expected_seqs):
self.assertEqual(taxon.label, expected_taxon)
self.assertEqual(char_matrix[taxon].symbols_as_string(), self.expected_seqs[expected_taxon])
def test_strict_interleaved(self):
s = """\
5 42
Turkey AAGCTNGGGC ATTTCAGGGT
Salmo gairAAGCCTTGGC AGTGCAGGGT
H. SapiensACCGGTTGGC CGTTCAGGGT
Chimp AAACCCTTGC CGTTACGCTT
Gorilla AAACCCTTGC CGGTACGCTT
GAGCCCGGGC AATACAGGGT AT
GAGCCGTGGC CGGGCACGGT AT
ACAGGTTGGC CGTTCAGGGT AA
AAACCGAGGC CGGGACACTC AT
AAACCATTGC CGGTACGCTT AA
"""
char_matrix = dendropy.DnaCharacterMatrix.get_from_string(
s,
"phylip",
interleaved=True,
strict=True)
self.assertEqual(len(char_matrix), len(self.expected_seqs))
self.assertEqual(len(char_matrix.taxon_namespace), len(self.expected_seqs))
for taxon, expected_taxon in zip(char_matrix, self.expected_seqs):
self.assertEqual(taxon.label, expected_taxon)
self.assertEqual(char_matrix[taxon].symbols_as_string(), self.expected_seqs[expected_taxon])
def test_strict_interleaved_with_bad_chars(self):
s = """\
5 42
Turkey AAGCTNGGGC ATTTCA3828GGGT
Salmo gairAAGCCTTGGC AGTGCA3828GGGT
H. SapiensACCGGTTGGC CGTTCA3828GGGT
Chimp AAACCCTTGC CGTTAC3828GCTT
Gorilla AAACCCTTGC CGGTAC3828GCTT
GAGCCCGGGC AATACAGGGT AT
GAGCCGTGGC CGGGCACGGT AT
ACAGGTTGGC CGTTCAGGGT AA
AAACCGAGGC CGGGACACTC AT
AAACCATTGC CGGTACGCTT AA
"""
char_matrix = dendropy.DnaCharacterMatrix.get_from_string(
s,
"phylip",
interleaved=True,
strict=True,
ignore_invalid_chars=True)
self.assertEqual(len(char_matrix), len(self.expected_seqs))
self.assertEqual(len(char_matrix.taxon_namespace), len(self.expected_seqs))
for taxon, expected_taxon in zip(char_matrix, self.expected_seqs):
self.assertEqual(taxon.label, expected_taxon)
self.assertEqual(char_matrix[taxon].symbols_as_string(), self.expected_seqs[expected_taxon])
class PhylipContinuousVariantsTestCases(dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.expected_seqs = collections.OrderedDict()
cls.expected_seqs["Turkey"] = [-231.6391 , 972.4189 , 626.6717 , -328.6811 , -213.5738 , 464.3897 , -91.3483 , 349.8176 , 333.4800 , 521.4970 ]
cls.expected_seqs["Salmo gair"] = [ 104.4199 , 669.7402 , -68.6082 , 975.4302 , -874.4510 , -191.3305 , -179.8437 , 655.5611 , -657.4532 , -563.7863 ]
cls.expected_seqs["H. Sapiens"] = [-613.2947 , -600.7053 , -700.5140 , 438.6092 , 615.5268 , 640.7933 , 503.8948 , -159.7922 , 866.8036 , 274.0275 ]
cls.expected_seqs["Chimp"] = [-654.7695 , 103.3806 , -971.8866 , 853.9164 , 653.5797 , 823.6672 , -476.6859 , 325.9331 , 456.0902 , -399.7095 ]
cls.expected_seqs["Gorilla"] = [-762.4904 , 808.3665 , 522.5775 , 250.6523 , -287.9786 , -995.4612 , 571.9263 , -793.3975 , -42.7027 , 186.8869 ]
def test_strict_sequential(self):
s = """\
5 10
Turkey -231.6391 972.4189 626.6717 -328.6811 -213.5738 464.3897 -91.3483 349.8176 333.4800 521.4970
Salmo gair 104.4199 669.7402 -68.6082 975.4302 -874.4510 -191.3305 -179.8437 655.5611 -657.4532 -563.7863
H. Sapiens-613.2947 -600.7053 -700.5140 438.6092 615.5268 640.7933 503.8948 -159.7922 866.8036 274.0275
Chimp -654.7695 103.3806 -971.8866 853.9164 653.5797 823.6672 -476.6859 325.9331 456.0902 -399.7095
Gorilla -762.4904 808.3665 522.5775 250.6523 -287.9786 -995.4612 571.9263 -793.3975 -42.7027 186.8869
"""
char_matrix = dendropy.ContinuousCharacterMatrix.get_from_string(
s,
"phylip",
strict=True)
self.assertEqual(len(char_matrix), len(self.expected_seqs))
self.assertEqual(len(char_matrix.taxon_namespace), len(self.expected_seqs))
for taxon, expected_taxon in zip(char_matrix, self.expected_seqs):
self.assertEqual(taxon.label, expected_taxon)
self.assertEqual(char_matrix[taxon].values(), self.expected_seqs[expected_taxon])
def test_strict_interleaved(self):
s = """\
5 10
Turkey -231.6391 972.4189 626.6717 -328.6811
Salmo gair 104.4199 669.7402 -68.6082 975.4302
H. Sapiens-613.2947 -600.7053 -700.5140 438.6092
Chimp -654.7695 103.3806 -971.8866 853.9164
Gorilla -762.4904 808.3665 522.5775 250.6523
-213.5738 464.3897 -91.3483 349.8176 333.4800 521.4970
-874.4510 -191.3305 -179.8437 655.5611 -657.4532 -563.7863
615.5268 640.7933 503.8948 -159.7922 866.8036 274.0275
653.5797 823.6672 -476.6859 325.9331 456.0902 -399.7095
-287.9786 -995.4612 571.9263 -793.3975 -42.7027 186.8869
"""
char_matrix = dendropy.ContinuousCharacterMatrix.get_from_string(
s,
"phylip",
interleaved=True,
strict=True)
self.assertEqual(len(char_matrix), len(self.expected_seqs))
self.assertEqual(len(char_matrix.taxon_namespace), len(self.expected_seqs))
for taxon, expected_taxon in zip(char_matrix, self.expected_seqs):
self.assertEqual(taxon.label, expected_taxon)
self.assertEqual(char_matrix[taxon].values(), self.expected_seqs[expected_taxon])
if __name__ == "__main__":
unittest.main()
|
