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')
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')
