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_name_type(self):
"""should return the (latin|common) name given a latin, common or ensembl
db prefix names"""
self.assertEqual(Species.getSpeciesName("human"), "H**o sapiens")
self.assertEqual(Species.getSpeciesName("homo_sapiens"), "H**o sapiens")
self.assertEqual(Species.getCommonName("Mus musculus"), "Mouse")
self.assertEqual(Species.getCommonName("mus_musculus"), "Mouse")
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_name_type(self):
"""should return the (latin|common) name given a latin, common or ensembl
db prefix names"""
self.assertEqual(Species.getSpeciesName("human"), "H**o sapiens")
self.assertEqual(Species.getSpeciesName("homo_sapiens"),
"H**o sapiens")
self.assertEqual(Species.getCommonName("Mus musculus"), "Mouse")
self.assertEqual(Species.getCommonName("mus_musculus"), "Mouse")
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 __init__(self, Species, Release, account=None, pool_recycle=None):
super(Genome, self).__init__()
assert Release, 'invalid release specified'
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
# TODO: check Release may not be necessary because: assert Release above
if Release is None:
Release = get_latest_release(account=account)
self._gen_release = None
# TODO make name and release immutable properties
self.Species = _Species.getSpeciesName(Species)
self.Release = str(Release)
# the db connections
self._core_db = None
self._var_db = None
self._other_db = None
self._feature_type_ids = FeatureTypeCache(self)
self._feature_coord_levels = FeatureCoordLevels(self.Species)
def __init__(self, Species, Release, account=None, pool_recycle=None):
super(Genome, self).__init__()
assert Release, 'invalid release specified'
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
# TODO: check Release may not be necessary because: assert Release above
if Release is None:
Release = get_latest_release(account=account)
self._gen_release = None
# TODO make name and release immutable properties
self.Species = _Species.getSpeciesName(Species)
self.Release = str(Release)
# the db connections
self._core_db = None
self._var_db = None
self._other_db = None
self._feature_type_ids = FeatureTypeCache(self)
self._feature_coord_levels = FeatureCoordLevels(self.Species)
def __repr__(self):
my_type = self.__class__.__name__
name = _Species.getCommonName(self.Species)
coord_type = self.CoordType
c = '%s(%r,%r,%r,%d-%d,%d)'%(my_type, name, coord_type,
self.CoordName, self.Start, self.End, self.Strand)
return c.replace("'", "")
def __repr__(self):
my_type = self.__class__.__name__
name = _Species.getCommonName(self.Species)
coord_type = self.CoordType
c = '%s(%r,%r,%r,%d-%d,%d)'%(my_type, name, coord_type,
self.CoordName, self.Start, self.End, self.Strand)
return c.replace("'", "")
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 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 _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 __call__(self,
species=None,
core_db=None,
feature_types=None,
var_db=None,
otherfeature_db=None):
if 'variation' in feature_types:
assert var_db is not None
species = _Species.getSpeciesName(core_db.db_name.Species or species)
self._set_species_feature_levels(species, core_db, feature_types,
var_db, otherfeature_db)
return self._species_feature_levels[species]
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 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 __init__(self, species, Release, account=None, pool_recycle=None, division=None):
assert Release, "invalid release specified"
self.Release = str(Release)
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
self._compara_db = None
sp = sorted([_Species.getSpeciesName(sp) for sp in set(species)])
self.Species = tuple(sp)
self._genomes = {}
self._attach_genomes()
self._species_id_map = None
self._species_db_map = None
self._species_set = None
self._method_species_link = None
self.division = division
def __call__(self, coord_type = None, core_db = None, species = None,
seq_level=False):
"""coord_type can be coord_type or coord_system_id"""
# TODO should only pass in core_db here, not that and Species, or just
# the genome - what if someone wants to compare different ensembl
# releases? keying by species is then a bad idea! better to key by
# id(object)
# change identifier to coord_system, handle either string val or int
# (see MySQL table) as is this shouldn't be a __call__, see line 168
# for reason why we should have a method to set data: setSpeciesCoord
# call then then just returns the coords for the named species
species = _Species.getSpeciesName(species or core_db.db_name.Species)
self._set_species_system(core_db, species)
if seq_level:
result = self._get_seq_level_system(species)
elif coord_type:
result = self._species_coord_systems[species][coord_type]
else:
result = self._species_coord_systems[species]
return result
def __call__(self, coord_type = None, core_db = None, species = None,
seq_level=False):
"""coord_type can be coord_type or coord_system_id"""
# TODO should only pass in core_db here, not that and Species, or just
# the genome - what if someone wants to compare different ensembl
# releases? keying by species is then a bad idea! better to key by
# id(object)
# change identifier to coord_system, handle either string val or int
# (see MySQL table) as is this shouldn't be a __call__, see line 168
# for reason why we should have a method to set data: setSpeciesCoord
# call then then just returns the coords for the named species
species = _Species.getSpeciesName(species or core_db.db_name.Species)
self._set_species_system(core_db, species)
if seq_level:
result = self._get_seq_level_system(species)
elif coord_type:
result = self._species_coord_systems[species][coord_type]
else:
result = self._species_coord_systems[species]
return result
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
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
def __init__(self,
species,
Release,
account=None,
pool_recycle=None,
division=None):
assert Release, 'invalid release specified'
self.Release = str(Release)
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
self._compara_db = None
sp = sorted([_Species.getSpeciesName(sp) for sp in set(species)])
self.Species = tuple(sp)
self._genomes = {}
self._attach_genomes()
self._species_id_map = None
self._species_db_map = None
self._species_set = None
self._method_species_link = None
self.division = division
def __init__(self, species):
self.Species = _Species.getSpeciesName(species)
def test_get_compara_name(self):
"""should correctly form valid names for assignment onto objects"""
self.assertEqual(Species.getComparaName('pika'), 'Pika')
self.assertEqual(Species.getComparaName('C.elegans'), 'Celegans')
self.assertEqual(Species.getComparaName('Caenorhabditis elegans'),
'Celegans')
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_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_get_compara_name(self):
"""should correctly form valid names for assignment onto objects"""
self.assertEqual(Species.getComparaName('pika'), 'Pika')
self.assertEqual(Species.getComparaName('C.elegans'), 'Celegans')
self.assertEqual(Species.getComparaName('Caenorhabditis elegans'),
'Celegans')
def getSyntenicRegions(self, Species=None, CoordName=None, Start=None,
End=None, Strand=1, ensembl_coord=False, region=None,
align_method=None, align_clade=None, method_clade_id=None):
"""returns a SyntenicRegions instance
Arguments:
- Species: the species name
- CoordName, Start, End, Strand: the coordinates for the region
- ensembl_coord: whether the coordinates are in Ensembl form
- region: a region instance or a location, in which case the
CoordName etc .. arguments are ignored
- align_method, align_clade: the alignment method and clade to use
Note: the options for this instance can be found by printing
the method_species_links attribute of this object.
- method_clade_id: over-rides align_method/align_clade. The entry
in method_species_links under method_link_species_set_id
"""
assert (align_method and align_clade) or method_clade_id, \
'Must specify (align_method & align_clade) or method_clade_id'
if method_clade_id is None:
for row in self.method_species_links:
if align_method.lower() in row['align_method'].lower() and\
align_clade.lower() in row['align_clade'].lower():
method_clade_id = row['method_link_species_set_id']
if method_clade_id is None:
raise RuntimeError, "Invalid align_method[%s] or align_clade "\
"specified[%s]" % (align_method, align_clade)
if region is None:
ref_genome = self._genomes[_Species.getSpeciesName(Species)]
region = ref_genome.makeLocation(CoordName=CoordName,
Start=Start, End=End, Strand=Strand,
ensembl_coord=ensembl_coord)
elif hasattr(region, 'Location'):
region = region.Location
# make sure the genome instances match
ref_genome = self._genomes[region.genome.Species]
if ref_genome is not region.genome:
# recreate region from our instance
region = ref_genome.makeLocation(CoordName=region.CoordName,
Start=region.Start, End=region.End,
Strand=region.Strand)
ref_dnafrag_id = self._get_dnafrag_id_for_coord(region)
blocks=self._get_genomic_align_blocks_for_dna_frag_id(method_clade_id,
ref_dnafrag_id, region)
for block in blocks:
genomic_align_block_id = block['genomic_align_block_id']
# we get joint records for these identifiers from
records = self._get_joint_genomic_align_dnafrag(
genomic_align_block_id)
members = []
ref_location = None
for record in records:
taxon_id = self.genome_taxon[record.genome_db_id]
genome = self.taxon_id_species[taxon_id]
# we have a case where we getback different coordinate system
# results for the ref genome. We keep only those that match
# the CoordName of region
if genome is region.genome and \
record.name == region.CoordName:
# this is the ref species and we adjust the ref_location
# for this block
diff_start = record.dnafrag_start-region.EnsemblStart
shift_start = [0, diff_start][diff_start > 0]
diff_end = record.dnafrag_end-region.EnsemblEnd
shift_end = [diff_end, 0][diff_end > 0]
try:
ref_location = region.resized(shift_start, shift_end)
except ValueError:
# we've hit some ref genome fragment that matches
# but whose coordinates aren't right
continue
elif genome is region.genome:
continue
members += [(genome, record)]
assert ref_location is not None, "Failed to make the reference"\
" location"
yield SyntenicRegions(self, members, ref_location=ref_location)
def __call__(self, species = None, core_db=None, feature_types=None, var_db=None, otherfeature_db=None):
if 'variation' in feature_types:
assert var_db is not None
species = _Species.getSpeciesName(core_db.db_name.Species or species)
self._set_species_feature_levels(species, core_db, feature_types, var_db, otherfeature_db)
return self._species_feature_levels[species]
def __init__(self, species):
self.Species = _Species.getSpeciesName(species)
def getSyntenicRegions(self,
Species=None,
CoordName=None,
Start=None,
End=None,
Strand=1,
ensembl_coord=False,
region=None,
align_method=None,
align_clade=None,
method_clade_id=None):
"""returns a SyntenicRegions instance
Arguments:
- Species: the species name
- CoordName, Start, End, Strand: the coordinates for the region
- ensembl_coord: whether the coordinates are in Ensembl form
- region: a region instance or a location, in which case the
CoordName etc .. arguments are ignored
- align_method, align_clade: the alignment method and clade to use
Note: the options for this instance can be found by printing
the method_species_links attribute of this object.
- method_clade_id: over-rides align_method/align_clade. The entry
in method_species_links under method_link_species_set_id
"""
assert (align_method and align_clade) or method_clade_id, \
'Must specify (align_method & align_clade) or method_clade_id'
if method_clade_id is None:
for row in self.method_species_links:
if align_method.lower() in row['align_method'].lower() and\
align_clade.lower() in row['align_clade'].lower():
method_clade_id = row['method_link_species_set_id']
if method_clade_id is None:
raise RuntimeError, "Invalid align_method[%s] or align_clade "\
"specified[%s]" % (align_method, align_clade)
if region is None:
ref_genome = self._genomes[_Species.getSpeciesName(Species)]
region = ref_genome.makeLocation(CoordName=CoordName,
Start=Start,
End=End,
Strand=Strand,
ensembl_coord=ensembl_coord)
elif hasattr(region, 'Location'):
region = region.Location
# make sure the genome instances match
ref_genome = self._genomes[region.genome.Species]
if ref_genome is not region.genome:
# recreate region from our instance
region = ref_genome.makeLocation(CoordName=region.CoordName,
Start=region.Start,
End=region.End,
Strand=region.Strand)
ref_dnafrag_id = self._get_dnafrag_id_for_coord(region)
blocks = self._get_genomic_align_blocks_for_dna_frag_id(
method_clade_id, ref_dnafrag_id, region)
for block in blocks:
genomic_align_block_id = block['genomic_align_block_id']
# we get joint records for these identifiers from
records = self._get_joint_genomic_align_dnafrag(
genomic_align_block_id)
members = []
ref_location = None
for record in records:
taxon_id = self.genome_taxon[record.genome_db_id]
genome = self.taxon_id_species[taxon_id]
# we have a case where we getback different coordinate system
# results for the ref genome. We keep only those that match
# the CoordName of region
if genome is region.genome and \
record.name == region.CoordName:
# this is the ref species and we adjust the ref_location
# for this block
diff_start = record.dnafrag_start - region.EnsemblStart
shift_start = [0, diff_start][diff_start > 0]
diff_end = record.dnafrag_end - region.EnsemblEnd
shift_end = [diff_end, 0][diff_end > 0]
try:
ref_location = region.resized(shift_start, shift_end)
except ValueError:
# we've hit some ref genome fragment that matches
# but whose coordinates aren't right
continue
elif genome is region.genome:
continue
members += [(genome, record)]
assert ref_location is not None, "Failed to make the reference"\
" location"
yield SyntenicRegions(self, members, ref_location=ref_location)
