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from cogent.db.ensembl.host import HostAccount, get_ensembl_account
from cogent.db.ensembl.compara import Compara, Genome
from cogent.util.unit_test import TestCase, main
__author__ = "Jason Merkin"
__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 = 12
account = HostAccount('mysql.ebi.ac.uk','anonymous', '', port=4157)
class MZ_ComparaTestBase(TestCase):
comp = Compara(['D.grimshawi', 'D.melanogaster'], Release=Release,
account=account, division='metazoa')
class MZ_TestCompara(MZ_ComparaTestBase):
def test_query_genome(self):
"""compara should attach valid genome attributes by common name"""
brca2 = self.comp.Dmelanogaster.getGeneByStableId("FBgn0050169")
self.assertEquals(brca2.Symbol.lower(), 'brca2')
def test_get_related_genes(self):
"""should correctly return the related gene regions from each genome"""
# using sc35, a splicing factor
sc35 = self.comp.Dmelanogaster.getGeneByStableId("FBgn0040286")
Orthologs = self.comp.getRelatedGenes(gene_region=sc35,
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"""
# here, it is brca2
brca2 = self.comp.Dmelanogaster.getGeneByStableId(
StableId='FBgn0050169')
orthologs = self.comp.getRelatedGenes(gene_region=brca2,
Relationship='ortholog_one2one')
self.assertEquals(len(orthologs.Members),2)
def test_get_collection(self):
sc35 = self.comp.Dmelanogaster.getGeneByStableId(StableId="FBgn0040286")
Orthologs = self.comp.getRelatedGenes(gene_region=sc35,
Relationship="ortholog_one2one")
collection = Orthologs.getSeqCollection()
self.assertTrue(len(collection.Seqs[0])> 1000)
class MZ_Genome(TestCase):
def test_get_general_release(self):
"""should correctly infer the general release"""
rel_lt_65 = Genome('D.melanogaster', Release=11, account=account)
self.assertEqual(rel_lt_65.GeneralRelease, 64)
self.assertEqual(rel_lt_65.CoreDb.db_name, 'drosophila_melanogaster_core_11_64_539')
rel_gt_65 = Genome('D.melanogaster', Release=13, account=account)
self.assertEqual(rel_gt_65.GeneralRelease, 66)
self.assertEqual(rel_gt_65.CoreDb.db_name, 'drosophila_melanogaster_core_13_66_539')
if __name__ == "__main__":
main()
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