本文整理汇总了Python中dark.titles.TitlesAlignments.sortTitles方法的典型用法代码示例。如果您正苦于以下问题：Python TitlesAlignments.sortTitles方法的具体用法？Python TitlesAlignments.sortTitles怎么用？Python TitlesAlignments.sortTitles使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类dark.titles.TitlesAlignments的用法示例。
在下文中一共展示了TitlesAlignments.sortTitles方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: testTitle
# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import sortTitles [as 别名]
def testTitle(self):
"""
Sorting on title must work.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('title')
self.assertEqual([
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
], result)示例2: testMaxScore_EValue
# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import sortTitles [as 别名]
def testMaxScore_EValue(self):
"""
Sorting on max score must work when scores are e values, including a
secondary sort on title.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('maxScore')
# self.assertEqual([
# 'gi|887699|gb|DQ37780 Cowpox virus 15', # 1e-6
# 'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 1e-7
# 'gi|887699|gb|DQ37780 Monkeypox virus 456', # 1e-8
# 'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 1e-10
# 'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 1e-11
# ], result)
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 1e-11
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 1e-10
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 1e-8
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 1e-7
'gi|887699|gb|DQ37780 Cowpox virus 15', # 1e-6
], result)示例3: testMedianScore_Bits
# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import sortTitles [as 别名]
def testMedianScore_Bits(self):
"""
Sorting on median score must work when scores are bit scores,
including a secondary sort on title.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n' + dumps(RECORD4) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
reads.add(Read('id4', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('medianScore')
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 25
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 20
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 20
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 20
'gi|887699|gb|DQ37780 Cowpox virus 15', # 20
], result)示例4: testLength
# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import sortTitles [as 别名]
def testLength(self):
"""
Sorting on sequence length must work, including a secondary sort on
title.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch('__builtin__.open', mockOpener, create=True):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('length')
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 38000
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 37000
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 35000
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 35000
'gi|887699|gb|DQ37780 Cowpox virus 15', # 30000
], result)示例5: testMedianScore_EValue
# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import sortTitles [as 别名]
def testMedianScore_EValue(self):
"""
Sorting on median score must work when scores are bit scores,
including a secondary sort on title.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n' + dumps(RECORD4) + '\n'))
with patch('__builtin__.open', mockOpener, create=True):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
reads.add(Read('id4', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('medianScore')
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 1e-11
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 1e-10
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 1e-8
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 1e-7
'gi|887699|gb|DQ37780 Cowpox virus 15', # worst :-)
], result)示例6: testEmpty
# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import sortTitles [as 别名]
def testEmpty(self):
"""
Sorting when there are no titles must return the empty list.
"""
mockOpener = mockOpen(read_data=dumps(PARAMS) + '\n')
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('title')
self.assertEqual([], result)