def test_no_assembly(self):
"""return N's for coordinates with no assembly"""
krat = Genome('Kangaroo rat', Release=58)
Start=24385
End=Start+100
region = krat.getRegion(CoordName='scaffold_13754', Start=Start,
End=End)
self.assertEquals(str(region.Seq), 'N' * (End-Start))
def test_no_assembly(self):
"""return N's for coordinates with no assembly"""
krat = Genome('Kangaroo rat', Release=58)
Start = 24385
End = Start + 100
region = krat.getRegion(CoordName='scaffold_13754',
Start=Start,
End=End)
self.assertEquals(str(region.Seq), 'N' * (End - Start))
class TestFeatureCoordLevels(TestCase):
def setUp(self):
self.chicken = Genome(Species='chicken',
Release=Release,
account=account)
def test_feature_levels(self):
ChickenFeatureLevels = FeatureCoordLevels('chicken')
chicken_feature_levels = ChickenFeatureLevels(
feature_types=['gene', 'cpg', 'est'],
core_db=self.chicken.CoreDb,
otherfeature_db=self.chicken.OtherFeaturesDb)
self.assertEquals(chicken_feature_levels['repeat'].levels,
['chromosome', 'scaffold'])
self.assertEquals(set(chicken_feature_levels['cpg'].levels),
set(['chromosome', 'scaffold']))
def test_repeat(self):
# use chicken genome as it need to do conversion
# chicken coordinate correspondent toRefSeq human IL2A region
coord = dict(CoordName=9, Start=21727352, End=21729141)
region = self.chicken.getRegion(**coord)
# repeat is recorded at contig level, strand is 0
repeats = region.getFeatures(feature_types='repeat')
expect = [("9", 21727499, 21727527), ("9", 21728009, 21728018),
("9", 21728169, 21728178)]
obs = []
for repeat in repeats:
loc = repeat.Location
obs.append((str(loc.CoordName), loc.Start, loc.End))
self.assertEquals(set(obs), set(expect))
def test_cpg(self):
# contain 3 CpG island recorded at chromosome level
coord1 = dict(CoordName=26, Start=105184, End=184346)
cpgs1 = self.chicken.getFeatures(feature_types='cpg', **coord1)
exp = [("26", 112153, 113139), ("26", 134125, 135050),
("26", 178899, 180227)]
obs = []
for cpg in cpgs1:
loc = cpg.Location
obs.append((str(loc.CoordName), loc.Start, loc.End))
self.assertEquals(set(obs), set(exp))
# test cpg features record at scaffold level:
coord2 = dict(CoordName='JH376196.1', Start=1, End=14640)
cpgs2 = self.chicken.getFeatures(feature_types='cpg', **coord2)
self.assertEquals(len(list(cpgs2)), 3)
class TestFeatureCoordLevels(TestCase):
def setUp(self):
self.chicken = Genome(Species='chicken', Release=Release,
account=account)
def test_feature_levels(self):
ChickenFeatureLevels = FeatureCoordLevels('chicken')
chicken_feature_levels = ChickenFeatureLevels(
feature_types=['gene', 'cpg', 'est'],
core_db=self.chicken.CoreDb,
otherfeature_db=self.chicken.OtherFeaturesDb)
self.assertEquals(chicken_feature_levels['repeat'].levels,
['chromosome', 'scaffold'])
self.assertEquals(set(chicken_feature_levels['cpg'].levels),
set(['chromosome', 'scaffold']))
def test_repeat(self):
# use chicken genome as it need to do conversion
# chicken coordinate correspondent toRefSeq human IL2A region
coord = dict(CoordName=9, Start=21727352, End=21729141)
region = self.chicken.getRegion(**coord)
# repeat is recorded at contig level, strand is 0
repeats = region.getFeatures(feature_types = 'repeat')
expect = [("9", 21727499, 21727527), ("9", 21728009, 21728018),
("9", 21728169, 21728178)]
obs = []
for repeat in repeats:
loc = repeat.Location
obs.append((str(loc.CoordName), loc.Start, loc.End))
self.assertEquals(set(obs), set(expect))
def test_cpg(self):
# contain 3 CpG island recorded at chromosome level
coord1 = dict(CoordName=26, Start=105184, End=184346)
cpgs1 = self.chicken.getFeatures(feature_types='cpg', **coord1)
exp = [("26", 112153, 113139), ("26", 134125, 135050),
("26", 178899, 180227)]
obs = []
for cpg in cpgs1:
loc = cpg.Location
obs.append((str(loc.CoordName), loc.Start, loc.End))
self.assertEquals(set(obs), set(exp))
# test cpg features record at scaffold level:
coord2 = dict(CoordName='JH376196.1', Start=1, End=14640)
cpgs2 = self.chicken.getFeatures(feature_types='cpg', **coord2)
self.assertEquals(len(list(cpgs2)), 3)
class TestFeatureCoordLevels(TestCase):
def setUp(self):
self.chicken = Genome(Species='chicken',
Release=Release,
account=account)
def test_feature_levels(self):
ChickenFeatureLevels = FeatureCoordLevels('chicken')
chicken_feature_levels = ChickenFeatureLevels(
feature_types=['gene', 'cpg', 'est'],
core_db=self.chicken.CoreDb,
otherfeature_db=self.chicken.OtherFeaturesDb)
self.assertEquals(chicken_feature_levels['repeat'].levels, ['contig'])
self.assertEquals(set(chicken_feature_levels['cpg'].levels),\
set(['contig', 'supercontig', 'chromosome']))
def test_repeat(self):
# use chicken genome as it need to do conversion
# chicken coordinate correspondent toRefSeq human IL2A region
coord = dict(CoordName=9, Start=23817146, End=23818935)
region = self.chicken.getRegion(**coord)
# repeat is recorded at contig level, strand is 0
repeats = region.getFeatures(feature_types='repeat')
expect = [("9", 23817293, 23817321), ("9", 23817803, 23817812),
("9", 23817963, 23817972)]
obs = []
for repeat in repeats:
loc = repeat.Location
obs.append((loc.CoordName, loc.Start, loc.End))
self.assertEquals(set(obs), set(expect))
def test_cpg(self):
# contain 3 CpG island recorded at chromosome level
coord1 = dict(CoordName=26, Start=110000, End=190000)
cpgs1 = self.chicken.getFeatures(feature_types='cpg', **coord1)
exp = [("26", 116969, 117955), ("26", 139769, 140694),
("26", 184546, 185881)]
obs = []
for cpg in cpgs1:
loc = cpg.Location
obs.append((loc.CoordName, loc.Start, loc.End))
self.assertEquals(set(exp), set(obs))
# test cpg features record at supercontig level:
coord2 = dict(CoordName='Un_random', Start=29434117, End=29439117)
cpgs2 = self.chicken.getFeatures(feature_types='cpg', **coord2)
self.assertEquals(len(list(cpgs2)), 1)
class TestFeatureCoordLevels(TestCase):
def setUp(self):
self.chicken = Genome(Species='chicken', Release=Release,
account=account)
def test_feature_levels(self):
ChickenFeatureLevels = FeatureCoordLevels('chicken')
chicken_feature_levels = ChickenFeatureLevels(
feature_types=['gene', 'cpg', 'est'],
core_db=self.chicken.CoreDb,
otherfeature_db=self.chicken.OtherFeaturesDb)
self.assertEquals(chicken_feature_levels['repeat'].levels, ['contig'])
self.assertEquals(set(chicken_feature_levels['cpg'].levels),\
set(['contig', 'supercontig', 'chromosome']))
def test_repeat(self):
# use chicken genome as it need to do conversion
# chicken coordinate correspondent toRefSeq human IL2A region
coord = dict(CoordName=9, Start=23817146, End=23818935)
region = self.chicken.getRegion(**coord)
# repeat is recorded at contig level, strand is 0
repeats = region.getFeatures(feature_types = 'repeat')
expect = [("9", 23817293, 23817321), ("9", 23817803, 23817812),
("9", 23817963, 23817972)]
obs = []
for repeat in repeats:
loc = repeat.Location
obs.append((loc.CoordName, loc.Start, loc.End))
self.assertEquals(set(obs), set(expect))
def test_cpg(self):
# contain 3 CpG island recorded at chromosome level
coord1 = dict(CoordName=26, Start=110000, End=190000)
cpgs1 = self.chicken.getFeatures(feature_types = 'cpg', **coord1)
exp = [("26", 116969, 117955), ("26", 139769, 140694),
("26", 184546, 185881)]
obs = []
for cpg in cpgs1:
loc = cpg.Location
obs.append((loc.CoordName, loc.Start, loc.End))
self.assertEquals(set(exp), set(obs))
# test cpg features record at supercontig level:
coord2 = dict(CoordName='Un_random', Start=29434117, End=29439117)
cpgs2 = self.chicken.getFeatures(feature_types='cpg', **coord2)
self.assertEquals(len(list(cpgs2)), 1)
