def testEmpty(self):
"""
When no intervals are given, the reduction should be for the full hit
width.
"""
adjuster = OffsetAdjuster()
self.assertEqual([], adjuster.adjustments())
self.assertEqual(0, adjuster.adjustOffset(0))
def testEmpty(self):
"""
When no intervals are given, the reduction should be for the full hit
width.
"""
adjuster = OffsetAdjuster()
self.assertEqual([], adjuster.adjustments())
self.assertEqual(0, adjuster.adjustOffset(0))
def testNoReads(self):
"""
When no reads are added to an interval, the reduction should be for
the full hit width.
"""
ri = ReadIntervals(64)
adjuster = OffsetAdjuster(ri)
self.assertEqual([(64, 58)], adjuster.adjustments())
self.assertEqual(6, adjuster.adjustOffset(64))
def testNoReads(self):
"""
When no reads are added to an interval, the reduction should be for
the full hit width.
"""
ri = ReadIntervals(64)
adjuster = OffsetAdjuster(ri)
self.assertEqual([(64, 58)], adjuster.adjustments())
self.assertEqual(6, adjuster.adjustOffset(64))
def testOneReadThatExceedsHitOnBothEnds(self):
"""
When one read is given that exceeds the hit at both ends, there should
be no length reductions.
"""
ri = ReadIntervals(106)
ri.add(-100, 200)
adjuster = OffsetAdjuster(ri)
self.assertEqual([], adjuster.adjustments())
self.assertEqual(106, adjuster.adjustOffset(106))
def testOneReadThatExactlyCoversHit(self):
"""
When one read is given that exactly covers the hit, there should
be no length reductions.
"""
ri = ReadIntervals(106)
ri.add(0, 106)
adjuster = OffsetAdjuster(ri)
self.assertEqual([], adjuster.adjustments())
self.assertEqual(106, adjuster.adjustOffset(106))
def testOneReadInMiddle(self):
"""
When one read is added to the middle of an interval, there should be
two reductions.
"""
ri = ReadIntervals(106)
ri.add(32, 42)
adjuster = OffsetAdjuster(ri)
self.assertEqual([(32, 27), (106, 58)], adjuster.adjustments())
self.assertEqual(106 - 27 - 58, adjuster.adjustOffset(106))
def testOneReadAtEnd(self):
"""
When one read is added to the end of an interval, there should be one
reduction for the empty section before the read.
"""
ri = ReadIntervals(228)
ri.add(128, 228)
adjuster = OffsetAdjuster(ri)
self.assertEqual([(128, 121)], adjuster.adjustments())
self.assertEqual(107, adjuster.adjustOffset(228))
def testOneReadBeforeStart(self):
"""
When one read is added to the start of an interval before zero, there
should be one reduction for the empty section after the read.
"""
ri = ReadIntervals(228)
ri.add(-10, 100)
adjuster = OffsetAdjuster(ri)
self.assertEqual([(228, 121)], adjuster.adjustments())
self.assertEqual(107, adjuster.adjustOffset(228))
def testOneReadThatExceedsHitOnBothEnds(self):
"""
When one read is given that exceeds the hit at both ends, there should
be no length reductions.
"""
ri = ReadIntervals(106)
ri.add(-100, 200)
adjuster = OffsetAdjuster(ri)
self.assertEqual([], adjuster.adjustments())
self.assertEqual(106, adjuster.adjustOffset(106))
def testOneReadThatExactlyCoversHit(self):
"""
When one read is given that exactly covers the hit, there should
be no length reductions.
"""
ri = ReadIntervals(106)
ri.add(0, 106)
adjuster = OffsetAdjuster(ri)
self.assertEqual([], adjuster.adjustments())
self.assertEqual(106, adjuster.adjustOffset(106))
def testOneReadAtEnd(self):
"""
When one read is added to the end of an interval, there should be one
reduction for the empty section before the read.
"""
ri = ReadIntervals(228)
ri.add(128, 228)
adjuster = OffsetAdjuster(ri)
self.assertEqual([
(128, 121),
], adjuster.adjustments())
self.assertEqual(107, adjuster.adjustOffset(228))
def testOneReadBeforeStart(self):
"""
When one read is added to the start of an interval before zero, there
should be one reduction for the empty section after the read.
"""
ri = ReadIntervals(228)
ri.add(-10, 100)
adjuster = OffsetAdjuster(ri)
self.assertEqual([
(228, 121),
], adjuster.adjustments())
self.assertEqual(107, adjuster.adjustOffset(228))
def testTwoReadsInMiddle(self):
"""
When two reads are added to the middle of an interval, there should be
three reductions (after first empty area, after 2nd empty area, after
final empty area.
"""
ri = ReadIntervals(132)
ri.add(32, 42)
ri.add(58, 68)
adjuster = OffsetAdjuster(ri)
self.assertEqual([
(32, 27),
(58, 12),
(132, 58),
], adjuster.adjustments())
self.assertEqual(132 - 27 - 12 - 58, adjuster.adjustOffset(132))
# Test an HSP at the beginning is unchanged.
hsp = HSP(10,
readEndInSubject=10,
readStartInSubject=0,
subjectEnd=10,
subjectStart=0)
adjuster.adjustHSP(hsp)
self.assertEqual(10, hsp.readEndInSubject)
self.assertEqual(0, hsp.readStartInSubject)
self.assertEqual(10, hsp.subjectEnd)
self.assertEqual(0, hsp.subjectStart)
# Test an HSP in the first read region.
hsp = HSP(10,
readEndInSubject=42,
readStartInSubject=32,
subjectEnd=40,
subjectStart=35)
adjuster.adjustHSP(hsp)
self.assertEqual(15, hsp.readEndInSubject)
self.assertEqual(5, hsp.readStartInSubject)
self.assertEqual(13, hsp.subjectEnd)
self.assertEqual(8, hsp.subjectStart)
# Test an HSP in the second read region.
hsp = HSP(10,
readEndInSubject=68,
readStartInSubject=58,
subjectEnd=66,
subjectStart=60)
adjuster.adjustHSP(hsp)
self.assertEqual(29, hsp.readEndInSubject)
self.assertEqual(19, hsp.readStartInSubject)
self.assertEqual(27, hsp.subjectEnd)
self.assertEqual(21, hsp.subjectStart)
def testOneReadInMiddle(self):
"""
When one read is added to the middle of an interval, there should be
two reductions.
"""
ri = ReadIntervals(106)
ri.add(32, 42)
adjuster = OffsetAdjuster(ri)
self.assertEqual([
(32, 27),
(106, 58),
], adjuster.adjustments())
self.assertEqual(106 - 27 - 58, adjuster.adjustOffset(106))
def testTwoReadsInMiddle(self):
"""
When two reads are added to the middle of an interval, there should be
three reductions (after first empty area, after 2nd empty area, after
final empty area.
"""
ri = ReadIntervals(132)
ri.add(32, 42)
ri.add(58, 68)
adjuster = OffsetAdjuster(ri)
self.assertEqual(
[
(32, 27),
(58, 12),
(132, 58),
],
adjuster.adjustments())
self.assertEqual(132 - 27 - 12 - 58, adjuster.adjustOffset(132))
# Test an HSP at the beginning is unchanged.
hsp = HSP(10, readEndInSubject=10, readStartInSubject=0,
subjectEnd=10, subjectStart=0)
adjuster.adjustHSP(hsp)
self.assertEqual(10, hsp.readEndInSubject)
self.assertEqual(0, hsp.readStartInSubject)
self.assertEqual(10, hsp.subjectEnd)
self.assertEqual(0, hsp.subjectStart)
# Test an HSP in the first read region.
hsp = HSP(10, readEndInSubject=42, readStartInSubject=32,
subjectEnd=40, subjectStart=35)
adjuster.adjustHSP(hsp)
self.assertEqual(15, hsp.readEndInSubject)
self.assertEqual(5, hsp.readStartInSubject)
self.assertEqual(13, hsp.subjectEnd)
self.assertEqual(8, hsp.subjectStart)
# Test an HSP in the second read region.
hsp = HSP(10, readEndInSubject=68, readStartInSubject=58,
subjectEnd=66, subjectStart=60)
adjuster.adjustHSP(hsp)
self.assertEqual(29, hsp.readEndInSubject)
self.assertEqual(19, hsp.readStartInSubject)
self.assertEqual(27, hsp.subjectEnd)
self.assertEqual(21, hsp.subjectStart)