def test_get_ensembl_format(self):
"""should take common or latin names and return the corresponding
ensembl db prefix"""
self.assertEqual(Species.getEnsemblDbPrefix("human"), "homo_sapiens")
self.assertEqual(Species.getEnsemblDbPrefix("mouse"), "mus_musculus")
self.assertEqual(Species.getEnsemblDbPrefix("Mus musculus"),
"mus_musculus")
def test_get_ensembl_format(self):
"""should take common or latin names and return the corresponding
ensembl db prefix"""
self.assertEqual(Species.getEnsemblDbPrefix("human"), "homo_sapiens")
self.assertEqual(Species.getEnsemblDbPrefix("mouse"), "mus_musculus")
self.assertEqual(Species.getEnsemblDbPrefix("Mus musculus"),
"mus_musculus")
def test_add_new_species(self):
"""should correctly add a new species/common combination and infer the
correct ensembl prefix"""
species_name, common_name = "Otolemur garnettii", "Bushbaby"
Species.amendSpecies(species_name, common_name)
self.assertEqual(Species.getSpeciesName(species_name), species_name)
self.assertEqual(Species.getSpeciesName("Bushbaby"), species_name)
self.assertEqual(Species.getSpeciesName(common_name), species_name)
self.assertEqual(Species.getCommonName(species_name), common_name)
self.assertEqual(Species.getCommonName("Bushbaby"), common_name)
self.assertEqual(Species.getEnsemblDbPrefix("Bushbaby"), "otolemur_garnettii")
self.assertEqual(Species.getEnsemblDbPrefix(species_name), "otolemur_garnettii")
self.assertEqual(Species.getEnsemblDbPrefix(common_name), "otolemur_garnettii")
def test_amend_existing(self):
"""should correctly amend an existing species"""
species_name = 'Ochotona princeps'
common_name1 = 'american pika'
common_name2 = 'pika'
ensembl_pref = 'ochotona_princeps'
Species.amendSpecies(species_name, common_name1)
self.assertEqual(Species.getCommonName(species_name),common_name1)
Species.amendSpecies(species_name, common_name2)
self.assertEqual(Species.getSpeciesName(common_name2), species_name)
self.assertEqual(Species.getSpeciesName(ensembl_pref), species_name)
self.assertEqual(Species.getCommonName(species_name), common_name2)
self.assertEqual(Species.getCommonName(ensembl_pref), common_name2)
self.assertEqual(Species.getEnsemblDbPrefix(species_name),ensembl_pref)
self.assertEqual(Species.getEnsemblDbPrefix(common_name2),ensembl_pref)
def test_add_new_species(self):
"""should correctly add a new species/common combination and infer the
correct ensembl prefix"""
species_name, common_name = "Otolemur garnettii", "Bushbaby"
Species.amendSpecies(species_name, common_name)
self.assertEqual(Species.getSpeciesName(species_name), species_name)
self.assertEqual(Species.getSpeciesName("Bushbaby"), species_name)
self.assertEqual(Species.getSpeciesName(common_name), species_name)
self.assertEqual(Species.getCommonName(species_name), common_name)
self.assertEqual(Species.getCommonName("Bushbaby"), common_name)
self.assertEqual(Species.getEnsemblDbPrefix("Bushbaby"),
"otolemur_garnettii")
self.assertEqual(Species.getEnsemblDbPrefix(species_name),
"otolemur_garnettii")
self.assertEqual(Species.getEnsemblDbPrefix(common_name),
"otolemur_garnettii")
def test_amend_existing(self):
"""should correctly amend an existing species"""
species_name = 'Ochotona princeps'
common_name1 = 'american pika'
common_name2 = 'pika'
ensembl_pref = 'ochotona_princeps'
Species.amendSpecies(species_name, common_name1)
self.assertEqual(Species.getCommonName(species_name), common_name1)
Species.amendSpecies(species_name, common_name2)
self.assertEqual(Species.getSpeciesName(common_name2), species_name)
self.assertEqual(Species.getSpeciesName(ensembl_pref), species_name)
self.assertEqual(Species.getCommonName(species_name), common_name2)
self.assertEqual(Species.getCommonName(ensembl_pref), common_name2)
self.assertEqual(Species.getEnsemblDbPrefix(species_name),
ensembl_pref)
self.assertEqual(Species.getEnsemblDbPrefix(common_name2),
ensembl_pref)
def make_db_name_pattern(species=None, db_type=None, release=None):
"""returns a pattern for matching the db name against"""
sep = r"%"
pattern = ""
if species:
species = Species.getEnsemblDbPrefix(species)
pattern = "%s%s" % (sep, species)
if db_type:
pattern = "%s%s%s" % (pattern, sep, db_type)
if release:
pattern = "%s%s%s" % (pattern, sep, release)
assert pattern
return "'%s%s'" % (pattern, sep)
def _get_dnafrag_id_for_coord(self, coord):
"""returns the dnafrag_id for the coordnate"""
dnafrag_table = self.ComparaDb.getTable('dnafrag')
genome_db_table = self.ComparaDb.getTable('genome_db')
# column renamed between versions
prefix = coord.genome.Species.lower()
if int(self.Release) > 58:
prefix = _Species.getEnsemblDbPrefix(prefix)
query = sql.select([dnafrag_table.c.dnafrag_id,
dnafrag_table.c.coord_system_name],
sql.and_(dnafrag_table.c.genome_db_id ==\
genome_db_table.c.genome_db_id,
genome_db_table.c.name == prefix,
dnafrag_table.c.name == coord.CoordName))
try:
record = asserted_one(query.execute().fetchall())
dnafrag_id = record['dnafrag_id']
except NoItemError:
raise RuntimeError, 'No DNA fragment identified'
return dnafrag_id
