本文整理匯總了Python中skbio.core.distance.DissimilarityMatrix.from_file方法的典型用法代碼示例。如果您正苦於以下問題：Python DissimilarityMatrix.from_file方法的具體用法？Python DissimilarityMatrix.from_file怎麽用？Python DissimilarityMatrix.from_file使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類skbio.core.distance.DissimilarityMatrix的用法示例。
在下文中一共展示了DissimilarityMatrix.from_file方法的8個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: test_round_trip_read_write
# 需要導入模塊: from skbio.core.distance import DissimilarityMatrix [as 別名]
# 或者: from skbio.core.distance.DissimilarityMatrix import from_file [as 別名]
def test_round_trip_read_write(self):
"""Test reading, writing, and reading again works as expected."""
for dm_f in self.dm_fs:
# Read.
dm1 = DissimilarityMatrix.from_file(dm_f)
# Write.
out_f = StringIO()
dm1.to_file(out_f)
out_f.seek(0)
# Read.
dm2 = DissimilarityMatrix.from_file(out_f)
self.assertEqual(dm1, dm2)示例2: test_from_file_with_file_path
# 需要導入模塊: from skbio.core.distance import DissimilarityMatrix [as 別名]
# 或者: from skbio.core.distance.DissimilarityMatrix import from_file [as 別名]
def test_from_file_with_file_path(self):
"""Should identify the filepath correctly and parse from it."""
# should fail with the expected exception
with self.assertRaises(DissimilarityMatrixFormatError):
DissimilarityMatrix.from_file(self.bad_dm_fp)
obs = DissimilarityMatrix.from_file(self.dm_2x2_asym_fp)
self.assertEqual(self.dm_2x2_asym, obs)
self.assertTrue(isinstance(obs, DissimilarityMatrix))
obs = DissimilarityMatrix.from_file(self.dm_3x3_fp)
self.assertEqual(self.dm_3x3, obs)
self.assertTrue(isinstance(obs, DissimilarityMatrix))示例3: test_from_file_real_file
# 需要導入模塊: from skbio.core.distance import DissimilarityMatrix [as 別名]
# 或者: from skbio.core.distance.DissimilarityMatrix import from_file [as 別名]
def test_from_file_real_file(self):
"""Should correctly parse a real on-disk file."""
self.tmp_f.write('\n'.join(DM_3x3_WHITESPACE_F))
self.tmp_f.seek(0)
obs = DissimilarityMatrix.from_file(self.tmp_f)
self.assertEqual(obs, self.dm_3x3)示例4: test_from_file_invalid_input
# 需要導入模塊: from skbio.core.distance import DissimilarityMatrix [as 別名]
# 或者: from skbio.core.distance.DissimilarityMatrix import from_file [as 別名]
def test_from_file_invalid_input(self):
"""Raises error on ill-formatted dissimilarity matrix file."""
# Empty dm.
with self.assertRaises(DissimilarityMatrixFormatError):
_ = DissimilarityMatrix.from_file([])
# Number of values don't match number of IDs.
with self.assertRaises(DissimilarityMatrixFormatError):
_ = DissimilarityMatrix.from_file(self.bad_dm_f1)
# Mismatched IDs.
with self.assertRaises(DissimilarityMatrixFormatError):
_ = DissimilarityMatrix.from_file(self.bad_dm_f2)
# Extra data at end.
with self.assertRaises(DissimilarityMatrixFormatError):
_ = DissimilarityMatrix.from_file(self.bad_dm_f3)
# Missing data.
with self.assertRaises(DissimilarityMatrixFormatError):
_ = DissimilarityMatrix.from_file(self.bad_dm_f4)
# Header, but no data.
with self.assertRaises(DissimilarityMatrixFormatError):
_ = DissimilarityMatrix.from_file(self.bad_dm_f5)
# Non-hollow.
with self.assertRaises(DissimilarityMatrixError):
_ = DissimilarityMatrix.from_file(self.bad_dm_f6)示例5: test_from_file_real_file
# 需要導入模塊: from skbio.core.distance import DissimilarityMatrix [as 別名]
# 或者: from skbio.core.distance.DissimilarityMatrix import from_file [as 別名]
def test_from_file_real_file(self):
"""Should correctly parse a real on-disk file."""
with tempfile.TemporaryFile(mode='r+',
prefix='skbio.core.tests.test_distance',
suffix='.txt') as fh:
fh.write('\n'.join(DM_3x3_WHITESPACE_F))
fh.seek(0)
obs = DissimilarityMatrix.from_file(fh)
self.assertEqual(obs, self.dm_3x3)示例6: test_from_file_list_of_strings
# 需要導入模塊: from skbio.core.distance import DissimilarityMatrix [as 別名]
# 或者: from skbio.core.distance.DissimilarityMatrix import from_file [as 別名]
def test_from_file_list_of_strings(self):
"""Should correctly parse a list of strings."""
obs = DissimilarityMatrix.from_file(DM_3x3_WHITESPACE_F)
self.assertEqual(obs, self.dm_3x3)示例7: test_from_file_extra_junk
# 需要導入模塊: from skbio.core.distance import DissimilarityMatrix [as 別名]
# 或者: from skbio.core.distance.DissimilarityMatrix import from_file [as 別名]
def test_from_file_extra_junk(self):
"""Should correctly parse a file with extra whitespace and comments."""
obs = DissimilarityMatrix.from_file(self.dm_3x3_whitespace_f)
self.assertEqual(obs, self.dm_3x3)示例8: test_from_file
# 需要導入模塊: from skbio.core.distance import DissimilarityMatrix [as 別名]
# 或者: from skbio.core.distance.DissimilarityMatrix import from_file [as 別名]
def test_from_file(self):
"""Should parse and return a valid DissimilarityMatrix given a file."""
for dm_f, dm in zip(self.dm_fs, self.dms):
obs = DissimilarityMatrix.from_file(dm_f)
self.assertEqual(obs, dm)