def test_contains(self):
"""Range contains an item if any span contains it"""
self.assertContains(self.one, 50)
self.assertContains(self.one, 0)
self.assertContains(self.one, 99)
self.assertNotContains(self.one, 100)
self.assertContains(self.three, 6)
self.assertNotContains(self.three, 7)
self.assertNotContains(self.three, 8)
self.assertNotContains(self.three, 14)
self.assertContains(self.three, 15)
self.assertNotContains(self.three, 29)
self.assertContains(self.three, 30)
self.assertContains(self.three, 34)
self.assertNotContains(self.three, 35)
self.assertNotContains(self.three, 40)
#should work if a span is added
self.three.Spans.append(40)
self.assertContains(self.three, 40)
#should work for spans
self.assertContains(self.three, Span(31, 33))
self.assertNotContains(self.three, Span(31, 37))
#span contains itself
self.assertContains(self.two, self.twocopy)
#should work for ranges
self.assertContains(self.three, Range([6, Span(15, 16), Span(30, 33)]))
#should work for copy, except when extra piece added
threecopy = Range(self.three)
self.assertContains(self.three, threecopy)
threecopy.Spans.append(1000)
self.assertNotContains(self.three, threecopy)
self.three.Spans.append(Span(950, 1050))
self.assertContains(self.three, threecopy)
self.assertNotContains(threecopy, self.three)
def test_init(self):
self.assertEqual(RangeFromString(''), Range())
self.assertEqual(RangeFromString(' 3 , 4\t, ,, 10 ,'),
Range([3, 4, 10]))
self.assertEqual(RangeFromString('3,4-10,1-5'),
Range([Span(3), Span(4, 10),
Span(1, 5)]))
def test_mapping(self):
"""Histogram Mapping should apply correct function to values"""
# bins, data, mapping
data = ['A','AAA','CCCCC','GGGGGGGGGGGGGG']
bins = [Span(0,2),Span(2,4),Span(4,6)]
mapping = Histogram(data=data,bins=bins,Mapping=len)
self.assertEqual(mapping._values, [['A'],['AAA'],['CCCCC']])
self.assertEqual(mapping.Other,['GGGGGGGGGGGGGG'])
def test_init_bins_data(self):
"""Histogram should fill bins with data if supplied"""
# most basic histogram, bins and data
data = [1,3,5,'A']
bins = [Span(0,2),Span(2,4),Span(4,6)]
data_and_bins = Histogram(data=data,bins=bins)
self.assertEqual(data_and_bins._bins,bins)
self.assertEqual(data_and_bins._values,[[1],[3],[5]])
self.assertEqual(data_and_bins.Other,['A'])
def test_call(self):
"""Histogram __call__ should update with new data"""
data = [1,3,5,'A']
bins = [Span(0,2),Span(2,4),Span(4,6)]
data_and_bins = Histogram(data=data,bins=bins)
#update the histogram
data_and_bins([4,5,6,7])
self.assertEqual(data_and_bins._values,[[1],[3],[5,4,5]])
self.assertEqual(data_and_bins.Other,['A',6,7])
def test_map(self):
"""reversing a map with multiple spans should preserve span relative
order"""
forward = [Span(20, 30), Span(40, 50)]
fmap = Map(spans=forward, parent_length=100)
fmap_reversed = fmap.nucleicReversed()
reverse = [Span(70, 80, Reverse=True), Span(50, 60, Reverse=True)]
rmap = Map(spans=reverse, parent_length=100)
for i in range(2):
self.assertEquals(fmap_reversed.spans[i], rmap.spans[i])
def setUp(self):
"""Set up a few standard ranges."""
self.one = Range(Span(0, 100))
self.two = Range([Span(3, 5), Span(8, 11)])
self.three = Range([Span(6, 7), Span(15, 17), Span(30, 35)])
self.overlapping = Range([Span(6, 10), Span(7, 3)])
self.single = Range(0)
self.singles = Range([3, 11])
self.twocopy = Range(self.two)
self.twothree = Range([self.two, self.three])
self.empty = Range([Span(6, 6), Span(8, 8)])
def test_multi(self):
"""Histogram Multi should allow values to match multiple bins"""
#bins, data, multi=True
bins2 = [Span(0,5),Span(3,8),Span(6,10)]
data2 = [0,1,2,3,4,5,6,7,8,9,10]
not_multi = Histogram(data2,bins2)
self.assertEqual(not_multi._values,[[0,1,2,3,4],[5,6,7],[8,9]])
self.assertEqual(not_multi.Other,[10])
multi = Histogram(data2,bins2,Multi=True)
self.assertEqual(multi._values,[[0,1,2,3,4],[3,4,5,6,7],[6,7,8,9]])
self.assertEqual(multi.Other,[10])
def test_clear(self):
"""Histogram clear should reset all data"""
data = [1,3,5,'A']
bins = [Span(0,2),Span(2,4),Span(4,6)]
data_and_bins = Histogram(data=data,bins=bins)
self.assertEqual(data_and_bins._bins,bins)
self.assertEqual(data_and_bins._values,[[1],[3],[5]])
self.assertEqual(data_and_bins.Other,['A'])
data_and_bins.clear()
self.assertEqual(data_and_bins._values,[[],[],[]])
self.assertEqual(data_and_bins.Other,[])
def test_endsAt(self):
"""Span endsAt should return True if input matches"""
e, f = self.empty, self.full
s = Span(30, 1000)
t = Span(-100, 35)
self.assertTrue(e.endsAt(0))
self.assertTrue(f.endsAt(35))
self.assertTrue(s.endsAt(1000))
self.assertFalse(f.endsAt(s))
self.assertFalse(s.endsAt(f))
self.assertTrue(f.endsAt(t))
self.assertTrue(t.endsAt(f))
def test_cmp(self):
"""Ranges should compare equal if they have the same spans"""
self.assertEqual(
self.twothree,
Range([
Span(3, 5),
Span(8, 11),
Span(6, 7),
Span(15, 17),
Span(30, 35)
]))
self.assertEqual(Range(), Range())
def test_startsAt(self):
"""Span startsAt should return True if input matches"""
e, f = self.empty, self.full
s = Span(30, 1000)
self.assertTrue(e.startsAt(0))
self.assertTrue(f.startsAt(30))
self.assertTrue(s.startsAt(30))
self.assertTrue(f.startsAt(s))
self.assertTrue(s.startsAt(f))
self.assertFalse(e.startsAt(f))
self.assertFalse(e.startsAt(-1))
self.assertFalse(e.startsAt(1))
self.assertFalse(f.startsAt(29))
def test_startsAt(self):
"""Span startsAt should return True if input matches"""
e, f = self.empty, self.full
s = Span(30, 1000)
self.assertTrue(e.startsAt(0))
self.assertTrue(f.startsAt(30))
self.assertTrue(s.startsAt(30))
self.assertTrue(f.startsAt(s))
self.assertTrue(s.startsAt(f))
self.assertFalse(e.startsAt(f))
self.assertFalse(e.startsAt(-1))
self.assertFalse(e.startsAt(1))
self.assertFalse(f.startsAt(29))
def test_endsInside(self):
"""Span endsInside should return True if input ends inside span"""
e, f, i, o = self.empty, self.full, self.inside, self.overlapping
self.assertFalse(e.endsInside(0))
self.assertFalse(f.endsInside(30))
self.assertFalse(f.endsInside(34))
self.assertFalse(f.endsInside(35))
self.assertFalse(e.endsInside(f))
self.assertTrue(i.endsInside(f))
self.assertFalse(f.endsInside(i))
self.assertFalse(o.endsInside(f))
self.assertFalse(o.endsInside(i))
self.assertTrue(e.endsInside(Span(-1, 1)))
self.assertTrue(e.endsInside(Span(0, 1)))
self.assertFalse(e.endsInside(Span(-1, 0)))
def test_toFreqs(self):
"""Histogram toFreqs() should return a Freqs object"""
h = Histogram(list(range(0,20)),bins=[Span(0,3),Span(3,10),
Span(10,18),Span(18,20)])
constructor=str
f = h.toFreqs()
self.assertEqual(f[constructor(Span(0,3))],3)
self.assertEqual(f[constructor(Span(3,10))],7)
self.assertEqual(f[constructor(Span(10,18))],8)
self.assertEqual(f[constructor(Span(18,20))],2)
def test_Extent(self):
"""Range extent should span limits of range"""
self.assertEqual(self.one.Extent, Span(0, 100))
self.assertEqual(self.three.Extent, Span(6, 35))
self.assertEqual(self.singles.Extent, Span(3, 12))
self.assertEqual(self.single.Extent, Span(0, 1))
self.three.Spans.append(Span(100, 105, Reverse=True))
self.assertEqual(self.three.Extent, Span(6, 105))
self.three.Spans.append(Span(-100, -1000))
self.assertEqual(self.three.Extent, Span(-1000, 105))
def setUp(self):
"""Define some standard Spans"""
self.empty = Range(Span(0, 0))
self.full = Range(Span(30, 35))
self.overlapping = Range(Span(32, 36))
self.inside = Range(Span(31, 32))
self.before = Range(Span(25, 30))
self.after = Range(Span(35, 40))
self.reverse = Range(Span(30, 35, Reverse=True))
self.spans_zero = Range(Span(-5, 5))
def test_Reverse(self):
"""Range Reverse property should return True if any span reversed"""
self.assertFalse(self.one.Reverse)
self.one.reverse()
self.assertTrue(self.one.Reverse)
self.assertFalse(self.two.Reverse)
self.two.Spans.append(Span(0, 100, Reverse=True))
self.assertTrue(self.two.Reverse)
self.two.reverse()
self.assertTrue(self.two.Reverse)
def test_reverse(self):
"""Range reverse method should reverse each span"""
for s in self.overlapping.Spans:
self.assertFalse(s.Reverse)
self.overlapping.reverse()
for s in self.overlapping.Spans:
self.assertTrue(s.Reverse)
self.overlapping.Spans.append(Span(0, 100))
self.overlapping.reverse()
for s in self.overlapping.Spans[0:1]:
self.assertFalse(s.Reverse)
self.assertTrue(self.overlapping.Spans[-1].Reverse)
def test_init(self):
"""Span object should init with Start, End, and Length"""
s = Span(0)
self.assertEqual(s.Start, 0)
self.assertEqual(s.End, 1)
self.assertEqual(s.Reverse, False)
#to get an empty interval, must specify start and end explicitly
t = Span(0, 0)
self.assertEqual(t.Start, 0)
self.assertEqual(t.End, 0)
self.assertEqual(t.Reverse, False)
#should be able to specify direction also
u = Span(5, 15, Reverse=True)
self.assertEqual(u.Start, 5)
self.assertEqual(u.End, 15)
self.assertEqual(u.Reverse, True)
#should be able to init from another span
v = Span(u)
self.assertEqual(v.Start, 5)
self.assertEqual(v.End, 15)
self.assertEqual(v.Reverse, True)
def test_endsAt(self):
"""Span endsAt should return True if input matches"""
e, f = self.empty, self.full
s = Span(30, 1000)
t = Span(-100, 35)
self.assertTrue(e.endsAt(0))
self.assertTrue(f.endsAt(35))
self.assertTrue(s.endsAt(1000))
self.assertFalse(f.endsAt(s))
self.assertFalse(s.endsAt(f))
self.assertTrue(f.endsAt(t))
self.assertTrue(t.endsAt(f))
def setUp(self):
"""Define some standard Spans"""
self.empty = Span(0, 0)
self.full = Span(35, 30) #will convert to (30, 35) internally
self.overlapping = Span(32, 36)
self.inside = Span(31, 32)
self.before = Span(25, 30)
self.after = Span(35, 40)
self.reverse = Span(30, 35, Reverse=True)
self.spans_zero = Span(-5, 5)
def cigar_to_map(cigar_text):
"""convert cigar string into Map"""
assert 'I' not in cigar_text
spans, posn = [], 0
for n, c in pattern.findall(cigar_text):
if n:
n = int(n)
else:
n = 1
if c == 'M':
spans.append(Span(posn, posn + n))
posn += n
else:
spans.append(LostSpan(n))
map = Map(spans=spans, parent_length=posn)
return map
def test_cmp(self):
"""Span cmp should support sort by 1st/2nd index and direction"""
s, e, f, r, i, o = self.spans_zero, self.empty, self.full, \
self.reverse, self.inside, self.overlapping
n = Span(30, 36)
expected_order = [s, e, f, r, n, i, o]
first = expected_order[:]
first.sort()
second = [r, o, f, s, e, i, n]
second.sort()
for i, j in zip(first, second):
self.assertSameObj(i, j)
for i, j in zip(first, expected_order):
self.assertSameObj(i, j)
def test_spans(self):
# a simple two part map of length 10
map = Map([(0, 5), (5, 10)], parent_length=10)
# try different spans on the above map
for ((start, end), expected) in [
((0, 4), "[0:4]"),
((0, 5), "[0:5]"),
((0, 6), "[0:5, 5:6]"),
((5, 10), "[5:10]"),
((-1, 10), "[-1-, 0:5, 5:10]"),
((5, 11), "[5:10, -1-]"),
((0, 10), "[0:5, 5:10]"),
((10, 0), "[10:5, 5:0]"),
]:
r = repr(Span(start, end, Reverse=start > end).remapWith(map))
#print (start, end), r,
if r != expected:
self.fail(repr((r, expected)))
def test_span(self):
length = 100
forward = Span(20, 30)
reverse = Span(70, 80, Reverse=True)
assert forward.reversedRelativeTo(100) == reverse
assert reverse.reversedRelativeTo(100) == forward
def setUp(self):
"""Define some standard Spans"""
self.empty = Span(0, 0)
self.full = Span(35, 30) #will convert to (30, 35) internally
self.overlapping = Span(32, 36)
self.inside = Span(31, 32)
self.before = Span(25, 30)
self.after = Span(35, 40)
self.reverse = Span(30, 35, Reverse=True)
self.spans_zero = Span(-5, 5)
def test_init(self):
"""Range init from Spans, numbers, or Ranges should work OK."""
#single span
self.assertEqual(self.one, Span(0, 100))
#list of spans
self.assertEqual(self.two.Spans, [Span(3, 5), Span(8, 11)])
#another range
self.assertEqual(self.two, self.twocopy)
#list of ranges
self.assertEqual(
self.twothree.Spans,
[Span(3, 5),
Span(8, 11),
Span(6, 7),
Span(15, 17),
Span(30, 35)])
#list of numbers
self.assertEqual(self.singles.Spans, [Span(3, 4), Span(11, 12)])
#single number
self.assertEqual(self.single.Spans, [Span(0, 1)])
#nothing
self.assertEqual(Range().Spans, [])
def test_init_bins(self):
"""Histogram should set _bins property correctly"""
bins = [Span(0,2),Span(2,4),Span(4,6)]
bins_only = Histogram(bins=bins)
self.assertEqual(bins_only._bins, bins)
def test_span(self):
length = 100
forward = Span(20, 30)
reverse = Span(70, 80, Reverse=True)
assert forward.reversedRelativeTo(100) == reverse
assert reverse.reversedRelativeTo(100) == forward
class SpanTests(TestCase):
"""Tests of the Span object."""
def setUp(self):
"""Define some standard Spans"""
self.empty = Span(0, 0)
self.full = Span(35, 30) #will convert to (30, 35) internally
self.overlapping = Span(32, 36)
self.inside = Span(31, 32)
self.before = Span(25, 30)
self.after = Span(35, 40)
self.reverse = Span(30, 35, Reverse=True)
self.spans_zero = Span(-5, 5)
def test_init(self):
"""Span object should init with Start, End, and Length"""
s = Span(0)
self.assertEqual(s.Start, 0)
self.assertEqual(s.End, 1)
self.assertEqual(s.Reverse, False)
#to get an empty interval, must specify start and end explicitly
t = Span(0, 0)
self.assertEqual(t.Start, 0)
self.assertEqual(t.End, 0)
self.assertEqual(t.Reverse, False)
#should be able to specify direction also
u = Span(5, 15, Reverse=True)
self.assertEqual(u.Start, 5)
self.assertEqual(u.End, 15)
self.assertEqual(u.Reverse, True)
#should be able to init from another span
v = Span(u)
self.assertEqual(v.Start, 5)
self.assertEqual(v.End, 15)
self.assertEqual(v.Reverse, True)
def test_contains(self):
"""Span object contains its start but not its end"""
self.assertNotContains(self.empty, 0)
self.assertContains(self.full, 30)
self.assertContains(self.full, 34)
self.assertNotContains(self.full, 35)
self.assertContains(self.full, self.inside)
self.assertNotContains(self.full, self.overlapping)
self.assertContains(self.spans_zero, 0)
self.assertContains(self.spans_zero, -5)
self.assertNotContains(self.spans_zero, 5)
def test_overlaps(self):
"""Span objects should be able to overlap points or spans"""
self.assertTrue(self.full.overlaps(self.overlapping))
self.assertFalse(self.full.overlaps(self.before))
self.assertFalse(self.before.overlaps(self.overlapping))
self.assertFalse(self.full.overlaps(self.after))
self.assertFalse(self.after.overlaps(self.before))
self.assertTrue(self.full.overlaps(self.inside))
self.assertTrue(self.spans_zero.overlaps(self.empty))
self.assertTrue(self.empty.overlaps(self.spans_zero))
def test_reverse(self):
"""Span reverse should change direction"""
self.assertFalse(self.empty.Reverse)
self.empty.reverse()
self.assertTrue(self.empty.Reverse)
self.empty.reverse()
self.assertFalse(self.empty.Reverse)
self.assertTrue(self.reverse.Reverse)
self.reverse.reverse()
self.assertFalse(self.reverse.Reverse)
def test_iter(self):
"""Span iter should loop through (integer) contents"""
self.assertEqual(list(iter(self.empty)), [])
self.assertEqual(list(iter(self.full)), [30,31,32,33,34])
self.assertEqual(list(iter(self.spans_zero)),[-5,-4,-3,-2,-1,0,1,2,3,4])
self.assertEqual(list(iter(self.inside)), [31])
self.assertEqual(list(self.reverse), [34,33,32,31,30])
def test_str(self):
"""Span str should print start, stop, reverse"""
self.assertEqual(str(self.empty), '(0,0,False)')
self.assertEqual(str(self.full), '(30,35,False)')
self.assertEqual(str(self.reverse), '(30,35,True)')
def test_len(self):
"""Span len should return difference between start and end"""
self.assertEqual(len(self.empty), 0)
self.assertEqual(len(self.full), 5)
self.assertEqual(len(self.inside),1)
self.assertEqual(len(self.spans_zero), 10)
def test_cmp(self):
"""Span cmp should support sort by 1st/2nd index and direction"""
s, e, f, r, i, o = self.spans_zero, self.empty, self.full, \
self.reverse, self.inside, self.overlapping
n = Span(30, 36)
expected_order = [s, e, f, r, n, i, o]
first = expected_order[:]
first.sort()
second = [r, o, f, s, e, i, n]
second.sort()
for i, j in zip(first, second):
self.assertSameObj(i, j)
for i, j in zip(first, expected_order):
self.assertSameObj(i, j)
def test_startsBefore(self):
"""Span startsBefore should match hand-calculated results"""
e, f = self.empty, self.full
self.assertTrue(e.startsBefore(f))
self.assertFalse(f.startsBefore(e))
self.assertTrue(e.startsBefore(1))
self.assertTrue(e.startsBefore(1000))
self.assertFalse(e.startsBefore(0))
self.assertFalse(e.startsBefore(-1))
self.assertFalse(f.startsBefore(30))
self.assertTrue(f.startsBefore(31))
self.assertTrue(f.startsBefore(1000))
def test_startsAfter(self):
"""Span startsAfter should match hand-calculated results"""
e, f = self.empty, self.full
self.assertFalse(e.startsAfter(f))
self.assertTrue(f.startsAfter(e))
self.assertFalse(e.startsAfter(1))
self.assertFalse(e.startsAfter(1000))
self.assertFalse(e.startsAfter(0))
self.assertTrue(e.startsAfter(-1))
self.assertTrue(f.startsAfter(29))
self.assertFalse(f.startsAfter(30))
self.assertFalse(f.startsAfter(31))
self.assertFalse(f.startsAfter(1000))
def test_startsAt(self):
"""Span startsAt should return True if input matches"""
e, f = self.empty, self.full
s = Span(30, 1000)
self.assertTrue(e.startsAt(0))
self.assertTrue(f.startsAt(30))
self.assertTrue(s.startsAt(30))
self.assertTrue(f.startsAt(s))
self.assertTrue(s.startsAt(f))
self.assertFalse(e.startsAt(f))
self.assertFalse(e.startsAt(-1))
self.assertFalse(e.startsAt(1))
self.assertFalse(f.startsAt(29))
def test_startsInside(self):
"""Span startsInside should return True if input starts inside span"""
e, f, i, o = self.empty, self.full, self.inside, self.overlapping
self.assertFalse(e.startsInside(0))
self.assertFalse(f.startsInside(30))
self.assertFalse(e.startsInside(f))
self.assertTrue(i.startsInside(f))
self.assertFalse(f.startsInside(i))
self.assertTrue(o.startsInside(f))
self.assertFalse(o.endsInside(i))
def test_endsBefore(self):
"""Span endsBefore should match hand-calculated results"""
e, f = self.empty, self.full
self.assertTrue(e.endsBefore(f))
self.assertFalse(f.endsBefore(e))
self.assertTrue(e.endsBefore(1))
self.assertTrue(e.endsBefore(1000))
self.assertFalse(e.endsBefore(0))
self.assertFalse(e.endsBefore(-1))
self.assertFalse(f.endsBefore(30))
self.assertFalse(f.endsBefore(31))
self.assertTrue(f.endsBefore(1000))
def test_endsAfter(self):
"""Span endsAfter should match hand-calculated results"""
e, f = self.empty, self.full
self.assertFalse(e.endsAfter(f))
self.assertTrue(f.endsAfter(e))
self.assertFalse(e.endsAfter(1))
self.assertFalse(e.endsAfter(1000))
self.assertFalse(e.endsAfter(0))
self.assertTrue(e.endsAfter(-1))
self.assertTrue(f.endsAfter(29))
self.assertTrue(f.endsAfter(30))
self.assertTrue(f.endsAfter(34))
self.assertFalse(f.endsAfter(35))
self.assertFalse(f.endsAfter(1000))
def test_endsAt(self):
"""Span endsAt should return True if input matches"""
e, f = self.empty, self.full
s = Span(30, 1000)
t = Span(-100, 35)
self.assertTrue(e.endsAt(0))
self.assertTrue(f.endsAt(35))
self.assertTrue(s.endsAt(1000))
self.assertFalse(f.endsAt(s))
self.assertFalse(s.endsAt(f))
self.assertTrue(f.endsAt(t))
self.assertTrue(t.endsAt(f))
def test_endsInside(self):
"""Span endsInside should return True if input ends inside span"""
e, f, i, o = self.empty, self.full, self.inside, self.overlapping
self.assertFalse(e.endsInside(0))
self.assertFalse(f.endsInside(30))
self.assertFalse(f.endsInside(34))
self.assertFalse(f.endsInside(35))
self.assertFalse(e.endsInside(f))
self.assertTrue(i.endsInside(f))
self.assertFalse(f.endsInside(i))
self.assertFalse(o.endsInside(f))
self.assertFalse(o.endsInside(i))
self.assertTrue(e.endsInside(Span(-1,1)))
self.assertTrue(e.endsInside(Span(0,1)))
self.assertFalse(e.endsInside(Span(-1,0)))
def test_simplify(self):
"""Range reduce should group overlapping ranges"""
#consolidate should have no effect when no overlap
r = self.two
r.simplify()
self.assertEqual(r.Spans, [Span(3, 5), Span(8, 11)])
#should consolidate an overlap of the same direction
r.Spans.append(Span(-1, 4))
r.simplify()
self.assertEqual(r.Spans, [Span(-1, 5), Span(8, 11)])
#should also consolidate _adjacent_ spans of the same direction
r.Spans.append(Span(11, 14))
r.simplify()
self.assertEqual(r.Spans, [Span(-1, 5), Span(8, 14)])
#bridge should cause consolidations
s = Range(r)
s.Spans.append(Span(5, 8))
s.simplify()
self.assertEqual(s.Spans, [Span(-1, 14)])
#ditto for bridge that overlaps everything
s = Range(r)
s.Spans.append(Span(-100, 100))
s.simplify()
self.assertEqual(s.Spans, [Span(-100, 100)])
#however, can't consolidate span in other orientation
s = Range(r)
s.Spans.append(Span(-100, 100, Reverse=True))
self.assertEqual(s.Spans, [Span(-1,5), Span(8,14), \
Span(-100,100,Reverse=True)])
def test_sort(self):
"""Range sort should sort component spans"""
one = self.one
one.sort()
self.assertEqual(one.Spans, [Span(100, 0)])
one.Spans.append(Span(-20, -10))
self.assertEqual(one.Spans, [Span(0, 100), Span(-20, -10)])
one.sort()
self.assertEqual(one.Spans, [Span(-20, -10), Span(0, 100)])
one.Spans.append(Span(-20, -10, Reverse=True))
self.assertEqual(
one.Spans,
[Span(-20, -10),
Span(0, 100),
Span(-20, -10, Reverse=True)])
one.sort()
self.assertEqual(
one.Spans,
[Span(-20, -10),
Span(-20, -10, Reverse=True),
Span(0, 100)])
def __init__(self, SeqId, Start, End=None):
"""Initializes location object"""
self.SeqId = SeqId
Span.__init__(self, Start, End)
def __init__(self, SeqId, Start, End=None):
"""Initializes location object"""
self.SeqId = SeqId
Span.__init__(self,Start, End)
def test_iter(self):
"""Range iter should iterate through each span in turn"""
self.assertEqual(list(iter(self.two)), [3, 4, 8, 9, 10])
self.two.Spans.insert(1, Span(103, 101, Reverse=True))
self.assertEqual(list(iter(self.two)), [3, 4, 102, 101, 8, 9, 10])