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from __future__ import division
import os
from cogent.util.unit_test import TestCase, main
from cogent.db.ensembl.host import HostAccount, get_ensembl_account
from cogent.db.ensembl.compara import Compara
__author__ = "Gavin Huttley, Hua Ying"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley", "hua Ying"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "alpha"
Release = 68
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)
def calc_slope(x1, y1, x2, y2):
"""computes the slope from two coordinate sets, assigning a delta of 1
when values are identical"""
delta_y = y2-y1
delta_x = x2-x1
delta_y = [delta_y, 1][delta_y == 0]
delta_x = [delta_x, 1][delta_x == 0]
return delta_y/delta_x
class ComparaTestBase(TestCase):
comp = Compara(['human', 'mouse', 'rat', 'platypus'], Release=Release,
account=account)
class TestCompara(ComparaTestBase):
def test_query_genome(self):
"""compara should attach valid genome attributes by common name"""
brca2 = self.comp.Mouse.getGeneByStableId("ENSMUSG00000041147")
self.assertEquals(brca2.Symbol.lower(), 'brca2')
def test_get_related_genes(self):
"""should correctly return the related gene regions from each genome"""
brca2 = self.comp.Mouse.getGeneByStableId("ENSMUSG00000041147")
Orthologs = self.comp.getRelatedGenes(gene_region=brca2,
Relationship="ortholog_one2one")
self.assertEquals("ortholog_one2one", Orthologs.Relationships[0])
def test_get_related_genes2(self):
"""should handle case where gene is absent from one of the genomes"""
clec2d = self.comp.Mouse.getGeneByStableId(
StableId='ENSMUSG00000030157')
orthologs = self.comp.getRelatedGenes(gene_region=clec2d,
Relationship='ortholog_one2many')
self.assertTrue(len(orthologs.Members) < 4)
def test_get_collection(self):
brca2 = self.comp.Human.getGeneByStableId(StableId="ENSG00000139618")
Orthologs = self.comp.getRelatedGenes(gene_region=brca2,
Relationship="ortholog_one2one")
collection = Orthologs.getSeqCollection()
self.assertTrue(len(collection.Seqs[0])> 1000)
def test_getting_alignment(self):
mid = "ENSMUSG00000041147"
brca2 = self.comp.Mouse.getGeneByStableId(StableId=mid)
result = list(self.comp.getSyntenicRegions(region=brca2,
align_method='PECAN', align_clade='vertebrates'))[0]
aln = result.getAlignment(feature_types='gene')
self.assertTrue(len(aln) > 1000)
def test_generate_method_clade_data(self):
"""should correctly determine the align_method align_clade options for
a group of species"""
# we should correctly infer the method_species_links, which is a
# cogent.util.Table instance
self.assertTrue(self.comp.method_species_links.Shape > (0,0))
def test_no_method_clade_data(self):
"""generate a Table with no rows if no alignment data"""
compara = Compara(['S.cerevisiae'], Release=Release, account=account)
self.assertEquals(compara.method_species_links.Shape[0], 0)
def test_get_syntenic_returns_nothing(self):
"""should correctly return None for a SyntenicRegion with golden-path
assembly gap"""
Start = 100000
End = Start + 100000
related = list(self.comp.getSyntenicRegions(Species='mouse',
CoordName='1', Start=Start, End=End,
align_method='PECAN', align_clade='vertebrates'))
self.assertEquals(related, [])
def test_get_species_set(self):
"""should return the correct set of species"""
expect = set(['Homo sapiens', 'Ornithorhynchus anatinus',
'Mus musculus', 'Rattus norvegicus'])
brca2 = self.comp.Human.getGeneByStableId(StableId="ENSG00000139618")
Orthologs = self.comp.getRelatedGenes(gene_region=brca2,
Relationship="ortholog_one2one")
self.assertEquals(Orthologs.getSpeciesSet(), expect)
def test_pool_connection(self):
"""excercising ability to specify pool connection"""
dog = Compara(['chimp', 'dog'], Release=Release, account=account,
pool_recycle=1000)
class TestSyntenicRegions(TestCase):
comp = Compara(['human', 'chimp', 'macaque'], account=account,
Release=Release)
def test_correct_alignments(self):
"""should return the correct alignments"""
# following cases have a mixture of strand between ref seq and others
coords_expected = [
[{'CoordName': 4, 'End': 78099, 'Species': 'human', 'Start': 77999, 'Strand':-1},
{'Homo sapiens:chromosome:4:77999-78099:-1':
'ATGTAAATCAAAACCAAAGTCTGCATTTATTTGCGGAAAGAGATGCTACATGTTCAAAGATAAATATGGAACATTTTTTAAAAGCATTCATGACTTAGAA',
'Macaca mulatta:chromosome:1:3891064-3891163:1':
'ATGTCAATCAAAACCAAAGTCTGTATTTATTTGCAGAAAGAGATACTGCATGTTCAAAGATAAATATGGAAC-TTTTTAAAAAGCATTAATGACTTATAC',
'Pan troglodytes:chromosome:4:102056-102156:-1':
'ATGTAAATCAAAACCAAAGTCTGCATTTATTTGCGGAAAGAGATGCTACATGTTCAAAGATAAATATGGAACATTTTTAAAAAGCATTCATGACTTAGAA'}],
[{'CoordName': 18, 'End': 213739, 'Species': 'human', 'Start': 213639, 'Strand':-1},
{'Homo sapiens:chromosome:18:213639-213739:-1':
'ATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGAGTGAGTGCAGATTATTCGGTAAACACT----CTTA',
'Macaca mulatta:chromosome:18:13858303-13858397:1':
'------GTTTCCCTTTAGGGCTCTAAGATGAGGTCATCATTGTTTTTAATCCTGAAGAAGGGCTACTGA----GTGCAGATTATTCTGTAAATGTGCTTACTTG',
'Pan troglodytes:chromosome:18:16601082-16601182:1':
'ATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGA----GTGCAGATTATTCTGTAAACACTCACTCTTA'}],
[{'CoordName': 5, 'End': 204974, 'Species': 'human', 'Start': 204874, 'Strand':1},
{'Homo sapiens:chromosome:5:204874-204974:1':
'AACACTTGGTATTT----CCCCTTTATGGAGTGAGAGAGATCTTTAAAATATAAACCCTTGATAATATAATATTACTACTTCCTATTA---CCTGTTATGCAGTTCT',
'Macaca mulatta:chromosome:6:1297736-1297840:-1':
'AACTCTTGGTGTTTCCTTCCCCTTTATGG---GAGAGAGATCTTTAAAATAAAAAACCTTGATAATATAATATTACTACTTTCTATTATCATCTGTTATGCAGTTCT',
'Pan troglodytes:chromosome:5:335911-336011:1':
'AACACTTGGTAGTT----CCCCTTTATGGAGTGAGAGAGATCTTTAAAATATAAACCCTTGATAATATAATATTACTACTTTCTATTA---CCTGTTATGCAGTTCT'}],
[{'CoordName': 18, 'End': 203270, 'Species': 'human', 'Start': 203170, 'Strand':-1},
{'Homo sapiens:chromosome:18:203170-203270:-1':
'GGAATAATGAAAGCAATTGTGAGTTAGCAATTACCTTCAAAGAATTACATTTCTTATACAAAGTAAAGTTCATTACTAACCTTAAGAACTTTGGCATTCA',
'Pan troglodytes:chromosome:18:16611584-16611684:1':
'GGAATAATGAAAGCAATTGTAAGTTAGCAATTACCTTCAAAGAATTACATTTCTTATACAAAGTAAAGTTCATTACTAACCTTAAGAACTTTGGCATTCA'}],
[{'CoordName': 2, 'End': 46445, 'Species': 'human', 'Start': 46345, 'Strand':-1},
{'Homo sapiens:chromosome:2:46345-46445:-1':
'CTACCACTCGAGCGCGTCTCCGCTGGACCCGGAACCCCGGTCGGTCCATTCCCCGCGAAGATGCGCGCCCTGGCGGCCCTGAGCGCGCCCCCGAACGAGC',
'Macaca mulatta:chromosome:13:43921-44021:-1':
'CTGCCACTCCAGCGCGTCTCCGCTGCACCCGGAGCGCCGGCCGGTCCATTCCCCGCGAGGATGCGCGCCCTGGCGGCCCTGAACACGTCGGCGAGAGAGC',
'Pan troglodytes:chromosome:2a:36792-36892:-1':
'CTACCACTCGAGCGCGTCTCCGCTGGACCCGGAACCCCAGTCGGTCCATTCCCCGCGAAGATGCGCGCCCTGGCGGCCCTGAACGCGCCCCCGAACGAGC'}],
[{'CoordName': 18, 'End': 268049, 'Species': 'human', 'Start': 267949, 'Strand':-1},
{'Homo sapiens:chromosome:18:267949-268049:-1':
'GCGCAGTGGCGGGCACGCGCAGCCGAGAAGATGTCTCCGACGCCGCCGCTCTTCAGTTTGCCCGAAGCGCGGACGCGGTTTACGGTGAGCTGTAGAGGGG',
'Macaca mulatta:chromosome:18:13805604-13805703:1':
'GCGCAG-GGCGGGCACGCGCAGCCGAGAAGATGTCTCCGACGCCGCCGCTCTTCAGTTTGCCCGAAGCGCGGACGCGGTTTACGGTGAGCTGTAGGCGGG',
'Pan troglodytes:chromosome:18:16546800-16546900:1':
'GCGCAGTGGCGGGCACGCGCAGCCGAGAAGATGTCTCCGACGCCGCCGCTCTTCAGTTTGCCCGAAGCGCGGACGCGGTTTACGGTGAGCTGTAGCGGGG'}],
[{'CoordName': 16, 'End': 107443, 'Species': 'human', 'Start': 107343, 'Strand':-1},
{'Homo sapiens:chromosome:16:107343-107443:-1':
'AAGAAGCAAACAGGTTTATTTTATACAGTGGGCCAGGCCGTGGGTCTGCCATGTGACTAGGGCATTTGGACCTAGGGAGAGGTCAGTCTCAGGCCAAGTA',
'Pan troglodytes:chromosome:16:48943-49032:-1':
'AAGAAGCAAACAGGTTTATTTTATACACTGGGCCAGGCCGTGGGTCTGCCATGTGACTAGGGAATTTGGACC-----------CAGTCTCAGGCCAAGTA'}]
]
# print self.comp.method_species_links
for coord, expect in coords_expected[1:]:
syntenic = list(
self.comp.getSyntenicRegions(method_clade_id=548, **coord))[0]
# check the slope computed from the expected and returned
# coordinates is ~ 1
got_names = dict([(n.split(':')[0], n.split(':')) for n in syntenic.getAlignment().Names])
exp_names = dict([(n.split(':')[0], n.split(':')) for n in expect.keys()])
for species in exp_names:
exp_chrom = exp_names[species][2]
got_chrom = got_names[species][2]
self.assertEquals(exp_chrom.lower(), got_chrom.lower())
exp_start, exp_end = map(int, exp_names[species][3].split('-'))
got_start, got_end = map(int, got_names[species][3].split('-'))
slope = calc_slope(exp_start, exp_end, got_start, got_end)
self.assertFloatEqual(abs(slope), 1.0, eps=1e-3)
def test_failing_region(self):
"""should correctly handle queries where multiple Ensembl have
genome block associations for multiple coord systems"""
gene = self.comp.Human.getGeneByStableId(StableId='ENSG00000188554')
# this should simply not raise any exceptions
syntenic_regions = list(self.comp.getSyntenicRegions(region=gene,
align_method='PECAN',
align_clade='vertebrates'))
if __name__ == "__main__":
main()
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