Python TitleAlignments.addAlignment方法代码示例

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
    def testResidueCountsOneReadTwoHSPsNotOverlapping(self):
        """
        The residueCounts method must return the correct result when just one
        read with two HSPs is aligned to a title and the HSPs do not overlap
        one another.

        HSP1:    ACGT
        HSP2:              CGTT
        """
        read = Read('id', 'ACGT')
        hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=0,
                   readEndInSubject=4, subjectStart=0, subjectEnd=4,
                   readMatchedSequence='ACGT', subjectMatchedSequence='ACGT')
        hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
                   readEndInSubject=14, subjectStart=10, subjectEnd=14,
                   readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
        titleAlignments = TitleAlignments('subject title', 55)
        titleAlignment = TitleAlignment(read, [hsp1, hsp2])
        titleAlignments.addAlignment(titleAlignment)
        self.assertEqual(
            {
                0: {'A': 1},
                1: {'C': 1},
                2: {'G': 1},
                3: {'T': 1},
                10: {'C': 1},
                11: {'G': 1},
                12: {'T': 1},
                13: {'T': 1},
            },
            titleAlignments.residueCounts())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testSummary(self):
     """
     The summary method must return the correct result.
     """
     titleAlignments = TitleAlignments('subject title', 10)
     titleAlignments.addAlignment(
         TitleAlignment(Read('id1', 'ACGT'), [
             HSP(30, subjectStart=0, subjectEnd=2),
         ]))
     titleAlignments.addAlignment(
         TitleAlignment(Read('id2', 'ACGT'), [
             HSP(55, subjectStart=2, subjectEnd=4),
             HSP(40, subjectStart=8, subjectEnd=9),
         ]))
     self.assertEqual(
         {
             'bestScore': 55,
             'coverage': 0.5,
             'hspCount': 3,
             'medianScore': 40,
             'readCount': 2,
             'subjectLength': 10,
             'subjectTitle': 'subject title',
         },
         titleAlignments.summary())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
    def testResidueCountsCaseConvertUpperIsDefault(self):
        """
        The residueCounts method must convert to uppercase by default.

        HSP1:       AcgT
        HSP2:        CGTT
        """
        read = Read('id', 'ACGT')
        hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
                   readEndInSubject=14, subjectStart=10, subjectEnd=14,
                   readMatchedSequence='AcgT', subjectMatchedSequence='ACGT')
        hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
                   readEndInSubject=15, subjectStart=11, subjectEnd=15,
                   readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
        titleAlignments = TitleAlignments('subject title', 55)
        titleAlignment = TitleAlignment(read, [hsp1, hsp2])
        titleAlignments.addAlignment(titleAlignment)
        self.assertEqual(
            {
                10: {'A': 1},
                11: {'C': 2},
                12: {'G': 2},
                13: {'T': 2},
                14: {'T': 1},
            },
            titleAlignments.residueCounts())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
    def testResidueCountsOneReadTwoHSPsNotAtStartOfSubject(self):
        """
        The residueCounts method must return the correct result when just one
        read with two HSPs is aligned to a title and the leftmost HSP is not
        aligned with the left edge of the subject.

        HSP1:       ACGT
        HSP2:        CGTT
        """
        read = Read('id', 'ACGT')
        hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
                   readEndInSubject=14, subjectStart=10, subjectEnd=14,
                   readMatchedSequence='ACGT', subjectMatchedSequence='ACGT')
        hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
                   readEndInSubject=15, subjectStart=11, subjectEnd=15,
                   readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
        titleAlignments = TitleAlignments('subject title', 55)
        titleAlignment = TitleAlignment(read, [hsp1, hsp2])
        titleAlignments.addAlignment(titleAlignment)
        self.assertEqual(
            {
                10: {'A': 1},
                11: {'C': 2},
                12: {'G': 2},
                13: {'T': 2},
                14: {'T': 1},
            },
            titleAlignments.residueCounts())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
    def testResidueCountsTwoReadsTwoHSPsLeftOverhang(self):
        """
        The residueCounts method must return the correct result when two
        reads, each with one HSP are aligned to a title and the leftmost HSP
        is aligned before the left edge of the subject (i.e, will include
        negative subject offsets).

        Subject:      GTT
        HSP1:       ACGT
        HSP2:        CGTT
        """
        read1 = Read('id', 'ACGT')
        hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=-2,
                   readEndInSubject=2, subjectStart=0, subjectEnd=2,
                   readMatchedSequence='GT', subjectMatchedSequence='GT')
        read2 = Read('id', 'CGTT')
        hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=-1,
                   readEndInSubject=3, subjectStart=0, subjectEnd=3,
                   readMatchedSequence='GTT', subjectMatchedSequence='GTT')
        titleAlignments = TitleAlignments('subject title', 55)
        titleAlignment = TitleAlignment(read1, [hsp1])
        titleAlignments.addAlignment(titleAlignment)
        titleAlignment = TitleAlignment(read2, [hsp2])
        titleAlignments.addAlignment(titleAlignment)
        self.assertEqual(
            {
                -2: {'A': 1},
                -1: {'C': 2},
                0: {'G': 2},
                1: {'T': 2},
                2: {'T': 1},
            },
            titleAlignments.residueCounts())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
    def testResidueCountsCaseConvertLower(self):
        """
        The residueCounts method must return the correct result when asked to
        convert residues to lower case.

        HSP1:       AcgT
        HSP2:        CGTT
        """
        read = Read('id', 'ACGT')
        hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
                   readEndInSubject=14, subjectStart=10, subjectEnd=14,
                   readMatchedSequence='AcgT', subjectMatchedSequence='ACGT')
        hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
                   readEndInSubject=15, subjectStart=11, subjectEnd=15,
                   readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
        titleAlignments = TitleAlignments('subject title', 55)
        titleAlignment = TitleAlignment(read, [hsp1, hsp2])
        titleAlignments.addAlignment(titleAlignment)
        self.assertEqual(
            {
                10: {'a': 1},
                11: {'c': 2},
                12: {'g': 2},
                13: {'t': 2},
                14: {'t': 1},
            },
            titleAlignments.residueCounts(convertCaseTo='lower'))

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testAddAlignment(self):
     """
     It must be possible to add an alignment to an instance of
     TitleAlignments.
     """
     titleAlignments = TitleAlignments('subject title', 55)
     read = Read('id', 'AAA')
     titleAlignment = TitleAlignment(read, [])
     titleAlignments.addAlignment(titleAlignment)
     self.assertEqual(read, titleAlignments[0].read)
     self.assertEqual([], titleAlignments[0].hsps)

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testMedianScoreWithNoHsps(self):
     """
     The medianScore function must raise ValueError if there are no HSPs.
     """
     titleAlignments = TitleAlignments('subject title', 55)
     read = Read('id1', 'AAA')
     titleAlignment = TitleAlignment(read, [])
     titleAlignments.addAlignment(titleAlignment)
     error = '^arg is an empty sequence$'
     six.assertRaisesRegex(self, ValueError, error,
                           titleAlignments.medianScore)

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testMedianScoreOfTwo(self):
     """
     The medianScore function must return the median score for the HSPs in
     all the alignments matching a title when given 2 scores.
     """
     hsp1 = HSP(7)
     hsp2 = HSP(15)
     titleAlignments = TitleAlignments('subject title', 55)
     read = Read('id1', 'AAA')
     titleAlignment = TitleAlignment(read, [hsp1, hsp2])
     titleAlignments.addAlignment(titleAlignment)
     self.assertEqual(11, titleAlignments.medianScore())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testFullCoverage(self):
     """
     The coverage method must return the correct value when the title is
     fully covered by its reads.
     """
     hsp1 = HSP(7, subjectStart=0, subjectEnd=50)
     hsp2 = HSP(8, subjectStart=50, subjectEnd=100)
     titleAlignments = TitleAlignments('subject title', 100)
     read = Read('id1', 'AAA')
     titleAlignment = TitleAlignment(read, [hsp1, hsp2])
     titleAlignments.addAlignment(titleAlignment)
     self.assertEqual(1.0, titleAlignments.coverage())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
    def makeTitleAlignments(self, *readIds):
        """
        Create a TitleAlignments instance containing reads with the
        ids given by C{ids}.

        param readIds: A C{list} of integer ids for reads.
        @return: A C{TitleAlignments} instance with reads with the given ids.
        """
        titleAlignments = TitleAlignments("subject title", 55)
        for readId in readIds:
            titleAlignment = TitleAlignment(Read("id" + str(readId), "A"), [])
            titleAlignments.addAlignment(titleAlignment)
        return titleAlignments

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testFullCoverageCounts(self):
     """
     The coverageCounts method must return the correct result when the title
     is fully covered by its reads.
     """
     hsp1 = HSP(7, subjectStart=0, subjectEnd=5)
     hsp2 = HSP(8, subjectStart=5, subjectEnd=10)
     titleAlignments = TitleAlignments('subject title', 10)
     read = Read('id1', 'AAA')
     titleAlignment = TitleAlignment(read, [hsp1, hsp2])
     titleAlignments.addAlignment(titleAlignment)
     c = Counter([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
     self.assertEqual(c, titleAlignments.coverageCounts())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testReadCount(self):
     """
     The readCount function must indicate how many reads matched a title.
     """
     hsp1 = HSP(7)
     hsp2 = HSP(14)
     hsp3 = HSP(21)
     titleAlignments = TitleAlignments('subject title', 55)
     read = Read('id1', 'AAA')
     titleAlignment = TitleAlignment(read, [hsp1, hsp2])
     titleAlignments.addAlignment(titleAlignment)
     read = Read('id2', 'AAA')
     titleAlignment = TitleAlignment(read, [hsp3])
     titleAlignments.addAlignment(titleAlignment)
     self.assertEqual(2, titleAlignments.readCount())

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testHSPs(self):
     """
     The hsps function must produce a list of all HSPs.
     """
     hsp1 = HSP(7)
     hsp2 = HSP(14)
     hsp3 = HSP(21)
     titleAlignments = TitleAlignments("subject title", 55)
     read = Read("id1", "AAA")
     titleAlignment = TitleAlignment(read, [hsp1, hsp2])
     titleAlignments.addAlignment(titleAlignment)
     read = Read("id2", "AAA")
     titleAlignment = TitleAlignment(read, [hsp3])
     titleAlignments.addAlignment(titleAlignment)
     self.assertEqual([7, 14, 21], [hsp.score.score for hsp in titleAlignments.hsps()])

# 需要导入模块: from dark.titles import TitleAlignments [as 别名]
# 或者: from dark.titles.TitleAlignments import addAlignment [as 别名]
 def testPartialCoverage(self):
     """
     The coverage method must return the correct value when the title is
     partially covered by its reads.
     """
     hsp1 = HSP(7, subjectStart=10, subjectEnd=20)
     hsp2 = HSP(15, subjectStart=30, subjectEnd=40)
     hsp3 = HSP(21, subjectStart=50, subjectEnd=60)
     titleAlignments = TitleAlignments('subject title', 100)
     read = Read('id1', 'AAA')
     titleAlignment = TitleAlignment(read, [hsp1, hsp2])
     titleAlignments.addAlignment(titleAlignment)
     read = Read('id2', 'AAA')
     titleAlignment = TitleAlignment(read, [hsp3])
     titleAlignments.addAlignment(titleAlignment)
     self.assertEqual(0.3, titleAlignments.coverage())