def test_gorilla(self):
"""should correctly return a gorilla gene"""
self.gorilla = Genome(Species="gorilla",
Release=Release,
account=account)
gene = self.gorilla.getGeneByStableId('ENSGGOG00000005730')
self.assertEquals(str(gene.Seq[:10]), 'TGGGAGTCCA')
class GenomeTestBase(TestCase):
human = Genome(Species="human", Release=Release, account=account)
mouse = Genome(Species="mouse", Release=Release, account=account)
rat = Genome(Species="rat", Release=Release, account=account)
macaq = Genome(Species="macaque", Release=Release, account=account)
gorilla = Genome(Species="gorilla", Release=Release, account=account)
brca2 = human.getGeneByStableId(StableId="ENSG00000139618")
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, ['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,
['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)
def _attach_genomes(self):
for species in self.Species:
attr_name = _Species.getComparaName(species)
genome = Genome(Species=species,
Release=self.Release,
account=self._account)
self._genomes[species] = genome
setattr(self, attr_name, genome)
def setUp(self):
self.chicken = Genome(Species='chicken', Release=Release,
account=account)
class TestGenome(GenomeTestBase):
def test_other_features(self):
"""should correctly return record for ENSESTG00000035043"""
est = self.human.getEstMatching(StableId='ENSESTG00000035043')
direct = list(est)[0]
ests = self.human.getFeatures(feature_types='est', CoordName=8,
Start=121470000, End=121600000)
stable_ids = [est.StableId for est in ests]
self.assertContains(stable_ids, direct.StableId)
def test_genome_comparison(self):
"""different genome instances with same CoreDb connection are equal"""
h2 = Genome(Species='human', Release=Release, account=account)
self.assertEquals(self.human, h2)
def test_make_location(self):
"""should correctly make a location for an entire chromosome"""
loc = self.human.makeLocation(CoordName=1)
self.assertEquals(len(loc), 249250621)
def test_get_region(self):
"""should return a generic region that extracts correct sequence"""
chrom = 1
Start = 11137
End = Start+20
region = self.human.getRegion(CoordName=chrom, Start=Start, End=End,
ensembl_coord=True)
self.assertEquals(region.Location.Start, Start-1)
self.assertEquals(region.Location.End, End)
self.assertEquals(region.Location.CoordName, str(chrom))
self.assertEquals(region.Location.CoordType, 'chromosome')
self.assertEquals(region.Seq, 'ACCTCAGTAATCCGAAAAGCC')
def test_get_assembly_exception_region(self):
"""should return correct sequence for region with an assembly
exception"""
##old:chrY:57767412-57767433; New: chrY:59358024-59358045
region = self.human.getRegion(CoordName = "Y", Start = 59358024,
End = 59358045, Strand = 1, ensembl_coord = True)
self.assertEquals(str(region.Seq), 'CGAGGACGACTGGGAATCCTAG')
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_getting_annotated_seq(self):
"""a region should return a sequence with the correct annotation"""
new_loc = self.brca2.Location.resized(-100, 100)
region = self.human.getRegion(region=new_loc)
annot_seq = region.getAnnotatedSeq(feature_types='gene')
gene_annots = annot_seq.getAnnotationsMatching('gene')
self.assertEquals(gene_annots[0].Name, self.brca2.Symbol)
def test_correct_feature_type_id_cache(self):
"""should obtain the feature type identifiers without failure"""
self.assertNotEquals(self.human._feature_type_ids.CpGisland, None)
def test_strand_conversion(self):
"""should consistently convert strand info"""
self.assertEquals(convert_strand(None), 1)
self.assertEquals(convert_strand(-1), -1)
self.assertEquals(convert_strand(1), 1)
self.assertEquals(convert_strand('-'), -1)
self.assertEquals(convert_strand('+'), 1)
self.assertEquals(convert_strand(-1.0), -1)
self.assertEquals(convert_strand(1.0), 1)
def test_pool_connection(self):
"""excercising ability to specify pool connection"""
dog = Genome(Species="dog", Release=Release, account=account,
pool_recycle=1000)
def test_gorilla(self):
"""should correctly return a gorilla gene"""
self.gorilla = Genome(Species="gorilla", Release=Release, account=account)
gene = self.gorilla.getGeneByStableId('ENSGGOG00000005730')
self.assertEquals(str(gene.Seq[:10]), 'TGGGAGTCCA')
def test_diff_strand_contig_chrom(self):
"""get correct sequence when contig and chromosome strands differ"""
gene = self.gorilla.getGeneByStableId('ENSGGOG00000001953')
cds = gene.CanonicalTranscript.Cds
self.assertEquals(str(cds), 'ATGGCCCAGGATCTCAGCGAGAAGGACCTGTTGAAGATG'
'GAGGTGGAGCAGCTGAAGAAAGAAGTGAAAAACACAAGAATTCCGATTTCCAAAGCGGGAAAGGAAAT'
'CAAAGAGTACGTGGAGGCCCAAGCAGGAAACGATCCTTTTCTCAAAGGCATCCCTGAGGACAAGAATC'
'CCTTCAAGGAGAAAGGTGGCTGTCTGATAAGCTGA')
def test_get_distinct_biotype(self):
"""Genome instance getDistinct for biotype should work on all genomes"""
for genome in self.gorilla, self.human, self.mouse, self.rat, self.macaq:
biotypes = genome.getDistinct('biotype')
def test_get_distinct_effect(self):
"""Genome instance getDistinct for SNP effect should work on all genomes"""
for genome in self.human, self.mouse, self.rat, self.macaq:
biotypes = genome.getDistinct('effect')
def test_gorilla(self):
"""should correctly return a gorilla gene"""
self.gorilla = Genome(Species="gorilla", Release=Release, account=account)
gene = self.gorilla.getGeneByStableId('ENSGGOG00000005730')
self.assertEquals(str(gene.Seq[:10]), 'TGGGAGTCCA')
def setUp(self):
self.chicken = Genome(Species='chicken', Release=Release,
account=account)
__email__ = "*****@*****.**"
__status__ = "alpha"
Release = 76
if 'ENSEMBL_ACCOUNT' in os.environ:
args = os.environ['ENSEMBL_ACCOUNT'].split()
host, username, password = args[0:3]
kwargs = {}
if len(args) > 3:
kwargs['port'] = int(args[3])
account = HostAccount(host, username, password, **kwargs)
else:
account = get_ensembl_account(release=Release)
human = Genome(Species='human', Release=Release, account=account)
platypus = Genome(Species='platypus', Release=Release, account=account)
class TestLocation(TestCase):
def test_init(self):
human_loc = Coordinate(CoordName='x',
Start=1000,
End=10000,
Strand=-1,
genome=human)
# TODO: complete test for platpus
self.assertEqual(human_loc.CoordType, 'chromosome')
self.assertEqual(human_loc.CoordName, 'x')
self.assertEqual(human_loc.Start, 1000)
self.assertEqual(human_loc.End, 10000)
class GenomeTestBase(TestCase):
human = Genome(Species="human", Release=Release, account=account)
mouse = Genome(Species="mouse", Release=Release, account=account)
rat = Genome(Species="rat", Release=Release, account=account)
macaq = Genome(Species="macaque", Release=Release, account=account)
brca2 = list(human.getGenesMatching(StableId="ENSG00000139618"))[0]
def test_pool_connection(self):
"""excercising ability to specify pool connection"""
dog = Genome(Species="dog",
Release=Release,
account=account,
pool_recycle=1000)
def test_genome_comparison(self):
"""different genome instances with same CoreDb connection are equal"""
h2 = Genome(Species='human', Release=Release, account=account)
self.assertEquals(self.human, h2)
class TestGenome(GenomeTestBase):
def test_other_features(self):
"""should correctly return record for ENSESTG00000000010"""
est = self.human.getEstMatching(StableId='ENSESTG00000000010')
direct = list(est)[0]
ests = self.human.getFeatures(feature_types='est',
CoordName=6,
Start=99994000,
End=100076519)
stable_ids = [est.StableId for est in ests]
self.assertContains(stable_ids, direct.StableId)
def test_genome_comparison(self):
"""different genome instances with same CoreDb connection are equal"""
h2 = Genome(Species='human', Release=Release, account=account)
self.assertEquals(self.human, h2)
def test_make_location(self):
"""should correctly make a location for an entire chromosome"""
loc = self.human.makeLocation(CoordName=1)
self.assertEquals(len(loc), 248956422)
def test_get_region(self):
"""should return a generic region that extracts correct sequence"""
chrom = 1
Start = 11137
End = Start + 20
region = self.human.getRegion(CoordName=chrom,
Start=Start,
End=End,
ensembl_coord=True)
self.assertEquals(region.Location.Start, Start - 1)
self.assertEquals(region.Location.End, End)
self.assertEquals(region.Location.CoordName, str(chrom))
self.assertEquals(region.Location.CoordType, 'chromosome')
self.assertEquals(region.Seq, 'ACCTCAGTAATCCGAAAAGCC')
def test_get_assembly_exception_region(self):
"""should return correct sequence for region with an assembly
exception"""
region = self.human.getRegion(CoordName="Y",
Start=57211873,
End=57211894,
Strand=1,
ensembl_coord=True)
self.assertEquals(str(region.Seq), 'CGAGGACGACTGGGAATCCTAG')
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_getting_annotated_seq(self):
"""a region should return a sequence with the correct annotation"""
new_loc = self.brca2.Location.resized(-100, 100)
region = self.human.getRegion(region=new_loc)
annot_seq = region.getAnnotatedSeq(feature_types='gene')
gene_annots = annot_seq.getAnnotationsMatching('gene')
self.assertEquals(gene_annots[0].Name, self.brca2.Symbol)
def test_correct_feature_type_id_cache(self):
"""should obtain the feature type identifiers without failure"""
self.assertNotEquals(self.human._feature_type_ids.CpGisland, None)
def test_strand_conversion(self):
"""should consistently convert strand info"""
self.assertEquals(convert_strand(None), 1)
self.assertEquals(convert_strand(-1), -1)
self.assertEquals(convert_strand(1), 1)
self.assertEquals(convert_strand('-'), -1)
self.assertEquals(convert_strand('+'), 1)
self.assertEquals(convert_strand(-1.0), -1)
self.assertEquals(convert_strand(1.0), 1)
def test_pool_connection(self):
"""excercising ability to specify pool connection"""
dog = Genome(Species="dog",
Release=Release,
account=account,
pool_recycle=1000)
def test_gorilla(self):
"""should correctly return a gorilla gene"""
self.gorilla = Genome(Species="gorilla",
Release=Release,
account=account)
gene = self.gorilla.getGeneByStableId('ENSGGOG00000005730')
self.assertEquals(str(gene.Seq[:10]), 'TGGGAGTCCA')
def test_diff_strand_contig_chrom(self):
"""get correct sequence when contig and chromosome strands differ"""
gene = self.gorilla.getGeneByStableId('ENSGGOG00000001953')
cds = gene.CanonicalTranscript.Cds
self.assertEquals(
str(cds), 'ATGGCCCAGGATCTCAGCGAGAAGGACCTGTTGAAGATG'
'GAGGTGGAGCAGCTGAAGAAAGAAGTGAAAAACACAAGAATTCCGATTTCCAAAGCGGGAAAGGAAAT'
'CAAAGAGTACGTGGAGGCCCAAGCAGGAAACGATCCTTTTCTCAAAGGCATCCCTGAGGACAAGAATC'
'CCTTCAAGGAGAAAGGTGGCTGTCTGATAAGCTGA')
def test_get_distinct_biotype(self):
"""Genome instance getDistinct for biotype should work on all genomes"""
for genome in self.gorilla, self.human, self.mouse, self.rat, self.macaq:
biotypes = genome.getDistinct('biotype')
def test_get_distinct_effect(self):
"""Genome instance getDistinct for SNP effect should work on all genomes"""
for genome in self.human, self.mouse, self.rat, self.macaq:
biotypes = genome.getDistinct('effect')
