Python TitlesAlignments.filter方法代码示例

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testCoverageIncludesSome(self):
     """
     The coverage function must return an titlesAlignments instance with
     only the expected titles if only some of its titles have sufficient
     coverage.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         # To understand why the following produces the result it does,
         # you need to look at the HSP coverage in sample_data.py and
         # calculate the coverage by hand.
         result = titlesAlignments.filter(minCoverage=0.0011)
         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.',
             ],
             sorted(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testFilterWithNoArguments(self):
     """
     The filter function must return a TitlesAlignments instance with all
     the titles of the original when called with no arguments.
     """
     mockOpener = mockOpen(read_data=(
         dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
         dumps(RECORD1) + '\n' + dumps(RECORD2) + '\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))
         readsAlignments = BlastReadsAlignments(reads, 'file.json')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter()
         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',
             ],
             sorted(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testCoverageIncludesAll(self):
     """
     The coverage function must return an titlesAlignments instance with
     all titles if all its titles has sufficient coverage.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(minCoverage=0.0)
         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',
             ],
             sorted(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testReadSetFilterAllowAnything(self):
     """
     The filter function work correctly when passed a 0.0 value for
     minNewReads, i.e. that considers any read set sufficiently novel.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(minNewReads=0.0)
         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',
             ],
             sorted(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testMinMedianScore_EValue(self):
     """
     The filter function work correctly when passed a value for
     minMedianScore when using e values.
     """
     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.filter(minMedianScore=1e-9)
         self.assertEqual(
             [
                 'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
                 'gi|887699|gb|DQ37780 Squirrelpox virus 55',
             ],
             sorted(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testMaxTitlesTwoSortOnLength(self):
     """
     The filter function must return the two titles whose sequences are the
     longest when maxTitles is 2 and sortOn is 'length'.
     """
     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 = DiamondReadsAlignments(reads, 'file.json',
                                                  'database.fasta')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(maxTitles=2, sortOn='length')
         self.assertEqual(
             [
                 'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
                 'gi|887699|gb|DQ37780 Squirrelpox virus 55',
             ],
             sorted(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testWithScoreBetterThan_EValue(self):
     """
     The filter function work correctly when passed a value for
     withScoreBetterThan when using e values.
     """
     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 = DiamondReadsAlignments(
             reads, 'file.json', 'database.fasta',
             scoreClass=LowerIsBetterScore)
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(withScoreBetterThan=1e-10)
         self.assertEqual(
             [
                 'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
             ],
             list(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testMaxTitlesZero(self):
     """
     The filter function must return an empty result when maxTitles is zero.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(maxTitles=0, sortOn='maxScore')
         self.assertEqual(0, len(result))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testCoverageExcludesAll(self):
     """
     The coverage function must return an titlesAlignments instance with
     no titles if none of its titles has sufficient coverage.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(minCoverage=0.1)
         self.assertEqual(0, len(result))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
    def testReadSetFilterStrict(self):
        """
        The filter function work correctly when passed a 1.0 value for
        minNewReads.
        """
        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 = DiamondReadsAlignments(reads, 'file.json',
                                                     'database.fasta')
            titlesAlignments = TitlesAlignments(readsAlignments)
            result = titlesAlignments.filter(minNewReads=1.0)

            # Either 'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.'
            # invalidates 'gi|887699|gb|DQ37780 Monkeypox virus 456' or
            # vice-versa. It depends on Python's dict walking order. Check
            # for both, making sure just one of them is true.

            mummypox = 'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.'
            monkeypox = 'gi|887699|gb|DQ37780 Monkeypox virus 456'

            assertionCount = 0
            if mummypox in result:
                self.assertTrue(monkeypox in
                                result.readSetFilter.invalidates(mummypox))
                assertionCount += 1
            if monkeypox in result:
                self.assertTrue(mummypox in
                                result.readSetFilter.invalidates(monkeypox))
                assertionCount += 1

            self.assertEqual(1, assertionCount)

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testMaxTitlesOne(self):
     """
     The filter function must return just the best title when maxTitles
     is one.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(maxTitles=1, sortOn='maxScore')
         self.assertEqual(
             [
                 'gi|887699|gb|DQ37780 Squirrelpox virus 55',
             ],
             sorted(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testWithScoreBetterThan_Bits(self):
     """
     The filter function work correctly when passed a value for
     withScoreBetterThan when using bit scores.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(withScoreBetterThan=24)
         self.assertEqual(
             [
                 'gi|887699|gb|DQ37780 Squirrelpox virus 55',
             ],
             list(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testMinMatchingReads(self):
     """
     The filter function work correctly when passed a value for
     minMatchingReads.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(minMatchingReads=2)
         self.assertEqual(
             [
                 'gi|887699|gb|DQ37780 Cowpox virus 15',
             ],
             list(result.keys()))

# 需要导入模块: from dark.titles import TitlesAlignments [as 别名]
# 或者: from dark.titles.TitlesAlignments import filter [as 别名]
 def testMinMedianScore_Bits(self):
     """
     The filter function work correctly when passed a value for
     minMedianScore when using bit scores.
     """
     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')
         titlesAlignments = TitlesAlignments(readsAlignments)
         result = titlesAlignments.filter(minMedianScore=22)
         self.assertEqual(
             [
                 'gi|887699|gb|DQ37780 Squirrelpox virus 55',
             ],
             result.keys())