Python ReadIntervals.add方法代码示例

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalExactCoveringCoverage(self):
     """
     If there is a single interval that spans the whole hit exactly,
     coverage should return 1.0.
     """
     ri = ReadIntervals(100)
     ri.add(0, 100)
     self.assertEqual(1.0, ri.coverage())

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalExactCovering(self):
     """
     If there is a single interval that spans the whole hit exactly, just
     that one interval should be returned by walk, and it should be full.
     """
     ri = ReadIntervals(100)
     ri.add(0, 100)
     self.assertEqual([(self.FULL, (0, 100))], list(ri.walk()))

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalCoveringAllExtendingLeftCoverage(self):
     """
     If there is a single interval that spans the whole hit, including
     going negative to the left, coverage should return 1.0.
     """
     ri = ReadIntervals(100)
     ri.add(-10, 100)
     self.assertEqual(1.0, ri.coverage())

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalCoveringAllExtendingRightCoverage(self):
     """
     If there is a single interval that spans the whole hit, including
     going beyond the hit to the right, coverage should return 1.0.
     """
     ri = ReadIntervals(100)
     ri.add(0, 110)
     self.assertEqual(1.0, ri.coverage())

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalStartingBeforeZeroCoverage(self):
     """
     If there is a single interval that starts before zero but doesn't
     cover the whole hit, coverage should return the correct value.
     """
     ri = ReadIntervals(100)
     ri.add(-50, 50)
     self.assertEqual(0.5, ri.coverage())

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalEndingAfterHitEndCoverage(self):
     """
     If there is a single interval that ends after the end of the hit
     but doesn't start at zero, coverage should return the correct value.
     """
     ri = ReadIntervals(100)
     ri.add(50, 150)
     self.assertEqual(0.5, ri.coverage())

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalEndingAfterHitEnd(self):
     """
     If there is a single interval that ends after the end of the hit
     but doesn't start at zero, we should get 2 intervals back from walk,
     an empty then a full.
     """
     ri = ReadIntervals(100)
     ri.add(50, 150)
     self.assertEqual([(self.EMPTY, (0, 50)), (self.FULL, (50, 150))], list(ri.walk()))

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalStartingBeforeZero(self):
     """
     If there is a single interval that starts before zero but doesn't
     cover the whole hit, we should get 2 intervals back from walk,
     a full one and then an empty.
     """
     ri = ReadIntervals(100)
     ri.add(-50, 50)
     self.assertEqual([(self.FULL, (-50, 50)), (self.EMPTY, (50, 100))], list(ri.walk()))

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalCoveringAllExtendingBoth(self):
     """
     If there is a single interval that spans the whole hit, including
     starting before zero and also going beyond the hit to the right, that
     one interval should be returned by walk, and it should be full.
     """
     ri = ReadIntervals(100)
     ri.add(-10, 110)
     self.assertEqual([(self.FULL, (-10, 110))], list(ri.walk()))

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalCoveringAllExtendingLeft(self):
     """
     If there is a single interval that spans the whole hit, including
     going negative to the left, that one interval should be returned by
     walk, and it should be full.
     """
     ri = ReadIntervals(100)
     ri.add(-10, 100)
     self.assertEqual([(self.FULL, (-10, 100))], list(ri.walk()))

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalExactCoveringCoverageCounts(self):
     """
     If there is a single interval that spans the whole hit exactly,
     coverageCounts should return the correct result.
     """
     ri = ReadIntervals(10)
     ri.add(0, 10)
     c = Counter([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
     self.assertEqual(c, ri.coverageCounts())

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def coverageCounts(self):
     """
     For each location in the title sequence, return a count of how many
     times that location is covered by a read.
     """
     intervals = ReadIntervals(self.subjectLength)
     for hsp in self.hsps():
         intervals.add(hsp.subjectStart, hsp.subjectEnd)
     return intervals.coverageCounts()

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
    def testOneIntervalInMiddle(self):
        """
        If there is a single interval in the middle of the hit, we
        should get 3 intervals back from walk: empty, full, empty.

        """
        ri = ReadIntervals(100)
        ri.add(50, 60)
        self.assertEqual([(self.EMPTY, (0, 50)), (self.FULL, (50, 60)), (self.EMPTY, (60, 100))], list(ri.walk()))

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
    def testOneIntervalInMiddleCoverage(self):
        """
        If there is a single interval in the middle of the hit, coverage
        should return the correct value.

        """
        ri = ReadIntervals(100)
        ri.add(50, 60)
        self.assertEqual(0.1, ri.coverage())

# 需要导入模块: from dark.intervals import ReadIntervals [as 别名]
# 或者: from dark.intervals.ReadIntervals import add [as 别名]
 def testOneIntervalInMiddleCoverageCounts(self):
     """
     If there is a single interval in the middle of the hit, coverageCounts
     should return the correct result.
     """
     ri = ReadIntervals(10)
     ri.add(5, 6)
     c = Counter([5])
     self.assertEqual(c, ri.coverageCounts())