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)