def _get_repeat_features(self, db, klass, target_coord, query_coord,
where_feature):
"""returns Repeat region instances"""
# we build repeats using coordinates from repeat_feature table
# the repeat_consensus_id is required to get the repeat name, class
# and type
repeat_feature_table = db.getTable('repeat_feature')
query = sql.select(
[repeat_feature_table],
repeat_feature_table.c.seq_region_id == query_coord.seq_region_id)
query = location_query(repeat_feature_table,
query_coord.EnsemblStart,
query_coord.EnsemblEnd,
query=query,
where=where_feature)
for record in query.execute():
coord = Coordinate(self,
CoordName=query_coord.CoordName,
Start=record['seq_region_start'],
End=record['seq_region_end'],
seq_region_id=record['seq_region_id'],
Strand=record['seq_region_strand'],
ensembl_coord=True)
if query_coord.CoordName != target_coord.CoordName:
coord = asserted_one(
get_coord_conversion(coord, target_coord.CoordType,
self.CoreDb))[1]
# coord = coord.makeRelativeTo(query_coord) #TODO: fix here if query_coord and target_coord have different coordName
# coord = coord.makeRelativeTo(target_coord, False)
yield klass(self,
db,
Location=coord,
Score=record['score'],
data=record)
def _get_simple_features(self, db, klass, target_coord, query_coord,
where_feature):
"""returns feature_type records for the query_coord from the
simple_feature table. The returned coord is referenced to
target_coord. At present, only CpG islands being queried."""
simple_feature_table = db.getTable('simple_feature')
feature_types = ['CpGisland']
feature_type_ids=[str(self._feature_type_ids.get(f)) for f in feature_types]
# fix the following
query = sql.select([simple_feature_table],
sql.and_(simple_feature_table.c.analysis_id.in_(feature_type_ids),
simple_feature_table.c.seq_region_id == query_coord.seq_region_id))
query = location_query(simple_feature_table,query_coord.EnsemblStart,
query_coord.EnsemblEnd, query=query,
where=where_feature)
records = query.execute()
for record in records:
coord = Coordinate(self, CoordName=query_coord.CoordName,
Start=record['seq_region_start'],
End = record['seq_region_end'],
seq_region_id=record['seq_region_id'],
Strand = record['seq_region_strand'],
ensembl_coord=True)
if query_coord.CoordName != target_coord.CoordName:
coord = asserted_one(get_coord_conversion(coord, target_coord.CoordType, self.CoreDb))[1]
# coord = coord.makeRelativeTo(query_coord) #TODO: fix here if query_coord and target_coord have different coordName
# coord = coord.makeRelativeTo(target_coord, False)
yield klass(self, db, Location=coord, Score=record['score'])
def _get_gene_features(self, db, klass, target_coord, query_coord,
where_feature):
"""returns all genes"""
xref_table = [None, db.getTable('xref')][db.Type == 'core']
gene_table = db.getTable('gene')
# after release 65, the gene_id_table is removed. The following is to maintain
# support for earlier releases.
if self.GeneralRelease >= 65:
gene_id_table = None
else:
gene_id_table = db.getTable('gene_stable_id')
# note gene records are at chromosome, not contig, level
condition = gene_table.c.seq_region_id == query_coord.seq_region_id
query = self._build_gene_query(db, condition, gene_table, gene_id_table, xref_table)
query = location_query(gene_table, query_coord.EnsemblStart,
query_coord.EnsemblEnd, query=query, where=where_feature)
for record in query.execute():
new = Coordinate(self, CoordName=query_coord.CoordName,
Start=record['seq_region_start'],
End = record['seq_region_end'],
Strand = record['seq_region_strand'],
seq_region_id=record['seq_region_id'],
ensembl_coord=True)
if query_coord.CoordName != target_coord.CoordName:
coord = asserted_one(get_coord_conversion(coord, target_coord.CoordType, self.CoreDb))[1]
# TODO: check coord, used 'new' here. where is coord (above line) used?
gene = klass(self, db, Location=new, data=record)
yield gene
def _get_repeat_features(self, db, klass, target_coord, query_coord, where_feature):
"""returns Repeat region instances"""
# we build repeats using coordinates from repeat_feature table
# the repeat_consensus_id is required to get the repeat name, class
# and type
repeat_feature_table = db.getTable("repeat_feature")
query = sql.select([repeat_feature_table], repeat_feature_table.c.seq_region_id == query_coord.seq_region_id)
query = location_query(
repeat_feature_table, query_coord.EnsemblStart, query_coord.EnsemblEnd, query=query, where=where_feature
)
for record in query.execute():
coord = Coordinate(
self,
CoordName=query_coord.CoordName,
Start=record["seq_region_start"],
End=record["seq_region_end"],
seq_region_id=record["seq_region_id"],
Strand=record["seq_region_strand"],
ensembl_coord=True,
)
if query_coord.CoordName != target_coord.CoordName:
coord = asserted_one(get_coord_conversion(coord, target_coord.CoordType, self.CoreDb))[1]
# coord = coord.makeRelativeTo(query_coord) #TODO: fix here if query_coord and target_coord have different coordName
# coord = coord.makeRelativeTo(target_coord, False)
yield klass(self, db, Location=coord, Score=record["score"], data=record)
def getFeatures(self,
region=None,
feature_types=None,
where_feature=None,
CoordName=None,
Start=None,
End=None,
Strand=None,
ensembl_coord=False):
"""returns Region instances for the specified location"""
if isinstance(feature_types, str):
feature_types = [feature_types]
feature_types = [ft.lower() for ft in feature_types]
feature_coord_levels = self._get_feature_coord_levels(feature_types)
if region is None:
seq_region_id = self._get_seq_region_id(CoordName)
region = Coordinate(self,
CoordName=CoordName,
Start=Start,
End=End,
Strand=convert_strand(Strand),
seq_region_id=seq_region_id,
ensembl_coord=ensembl_coord)
elif hasattr(region, 'Location'):
region = region.Location
coord = region
# the coordinate system at which locations are to be referenced, and
# the processing function
target_coords_funcs = \
dict(cpg = (self._get_simple_features, CpGisland),
repeat = (self._get_repeat_features, Repeat),
gene = (self._get_gene_features, Gene),
est = (self._get_gene_features, Est),
variation = (self._get_variation_features, Variation))
known_types = set(target_coords_funcs.keys())
if not set(feature_types) <= known_types:
raise RuntimeError, 'Unknown feature[%s], valid feature_types \
are: %s' % (set(feature_types) ^ known_types, known_types)
for feature_type in feature_types:
target_func, target_class = target_coords_funcs[feature_type]
db = self.CoreDb
if feature_type == 'est':
db = self.OtherFeaturesDb
feature_coords = feature_coord_levels[feature_type].levels
for feature_coord in feature_coords:
chrom_other_coords = get_coord_conversion(coord,
feature_coord,
db,
where=where_feature)
for chrom_coord, other_coord in chrom_other_coords:
for region in target_func(db, target_class, chrom_coord,
other_coord, where_feature):
yield region
def test_get_coord_conversion(self):
"""should correctly map between different coordinate levels"""
# not really testing the contig coordinates are correct
CoordName, Start, End, Strand = '1', 1000, 1000000, 1
human_loc = Coordinate(CoordName = CoordName, Start = Start, End = End,
Strand = Strand, genome = human)
results = get_coord_conversion(human_loc, 'contig', human.CoreDb)
for result in results:
self.assertTrue(result[0].CoordName == CoordName)
self.assertTrue(result[0].Start >= Start)
self.assertTrue(result[0].End <= End)
self.assertTrue(result[0].Strand == Strand)
def test_get_coord_conversion(self):
"""should correctly map between different coordinate levels"""
# not really testing the contig coordinates are correct
CoordName, Start, End, Strand = '1', 1000, 1000000, 1
human_loc = Coordinate(CoordName=CoordName,
Start=Start,
End=End,
Strand=Strand,
genome=human)
results = get_coord_conversion(human_loc, 'contig', human.CoreDb)
for result in results:
self.assertTrue(result[0].CoordName == CoordName)
self.assertTrue(result[0].Start >= Start)
self.assertTrue(result[0].End <= End)
self.assertTrue(result[0].Strand == Strand)
def getFeatures(self, region=None, feature_types=None, where_feature=None,
CoordName=None, Start=None, End=None, Strand=None,
ensembl_coord=False):
"""returns Region instances for the specified location"""
if isinstance(feature_types, str):
feature_types = [feature_types]
feature_types = [ft.lower() for ft in feature_types]
feature_coord_levels = self._get_feature_coord_levels(feature_types)
if region is None:
seq_region_id = self._get_seq_region_id(CoordName)
region = Coordinate(self,CoordName=CoordName, Start=Start,
End=End,
Strand = convert_strand(Strand),
seq_region_id=seq_region_id,
ensembl_coord=ensembl_coord)
elif hasattr(region, 'Location'):
region = region.Location
coord = region
# the coordinate system at which locations are to be referenced, and
# the processing function
target_coords_funcs = \
dict(cpg = (self._get_simple_features, CpGisland),
repeat = (self._get_repeat_features, Repeat),
gene = (self._get_gene_features, Gene),
est = (self._get_gene_features, Est),
variation = (self._get_variation_features, Variation))
known_types = set(target_coords_funcs.keys())
if not set(feature_types) <= known_types:
raise RuntimeError, 'Unknown feature[%s], valid feature_types \
are: %s' % (set(feature_types)^known_types, known_types)
for feature_type in feature_types:
target_func, target_class = target_coords_funcs[feature_type]
db = self.CoreDb
if feature_type == 'est':
db = self.OtherFeaturesDb
feature_coords = feature_coord_levels[feature_type].levels
for feature_coord in feature_coords:
chrom_other_coords = get_coord_conversion(coord, feature_coord,
db, where=where_feature)
for chrom_coord, other_coord in chrom_other_coords:
for region in target_func(db, target_class, chrom_coord,
other_coord, where_feature):
yield region
def _get_simple_features(self, db, klass, target_coord, query_coord,
where_feature):
"""returns feature_type records for the query_coord from the
simple_feature table. The returned coord is referenced to
target_coord. At present, only CpG islands being queried."""
simple_feature_table = db.getTable('simple_feature')
feature_types = ['CpGisland']
feature_type_ids = [
self._feature_type_ids.get(f) for f in feature_types
]
# fix the following
query = sql.select(
[simple_feature_table],
sql.and_(
simple_feature_table.c.analysis_id.in_(feature_type_ids),
simple_feature_table.c.seq_region_id ==
query_coord.seq_region_id))
query = location_query(simple_feature_table,
query_coord.EnsemblStart,
query_coord.EnsemblEnd,
query=query,
where=where_feature)
records = query.execute()
for record in records:
coord = Coordinate(self,
CoordName=query_coord.CoordName,
Start=record['seq_region_start'],
End=record['seq_region_end'],
seq_region_id=record['seq_region_id'],
Strand=record['seq_region_strand'],
ensembl_coord=True)
if query_coord.CoordName != target_coord.CoordName:
coord = asserted_one(
get_coord_conversion(coord, target_coord.CoordType,
self.CoreDb))[1]
# coord = coord.makeRelativeTo(query_coord) #TODO: fix here if query_coord and target_coord have different coordName
# coord = coord.makeRelativeTo(target_coord, False)
yield klass(self, db, Location=coord, Score=record['score'])
def _get_sequence_from_direct_assembly(coord=None, DEBUG=False):
# TODO clean up use of a coord
genome = coord.genome
# no matter what strand user provide, we get the + sequence first
coord.Strand = 1
species = genome.Species
coord_type = CoordSystem(species=species,
core_db=genome.CoreDb,
seq_level=True)
if DEBUG:
print('Created Coordinate:', coord, coord.EnsemblStart,
coord.EnsemblEnd)
print(coord.CoordType, coord_type)
assemblies = get_coord_conversion(coord, coord_type, genome.CoreDb)
if not assemblies:
raise NoItemError('no assembly for %s' % coord)
dna = genome.CoreDb.getTable('dna')
seqs, positions = [], []
for q_loc, t_loc in assemblies:
assert q_loc.Strand == 1
length = len(t_loc)
# get MySQL to do the string slicing via substr function
query = sql.select([
substr(dna.c.sequence, t_loc.EnsemblStart,
length).label('sequence')
], dna.c.seq_region_id == t_loc.seq_region_id)
record = asserted_one(query.execute().fetchall())
seq = record['sequence']
seq = DNA.makeSequence(seq)
if t_loc.Strand == -1:
seq = seq.rc()
seqs.append(str(seq))
positions.append((q_loc.Start, q_loc.End))
sequence = _assemble_seq(seqs, coord.Start, coord.End, positions)
return sequence
def _get_sequence_from_direct_assembly(coord=None, DEBUG=False):
# TODO clean up use of a coord
genome = coord.genome
# no matter what strand user provide, we get the + sequence first
coord.Strand = 1
species = genome.Species
coord_type = CoordSystem(species=species,core_db=genome.CoreDb,
seq_level=True)
if DEBUG:
print 'Created Coordinate:',coord,coord.EnsemblStart,coord.EnsemblEnd
print coord.CoordType, coord_type
assemblies = get_coord_conversion(coord, coord_type, genome.CoreDb)
if not assemblies:
raise NoItemError, 'no assembly for %s' % coord
dna = genome.CoreDb.getTable('dna')
seqs, positions = [], []
for q_loc, t_loc in assemblies:
assert q_loc.Strand == 1
length = len(t_loc)
# get MySQL to do the string slicing via substr function
query = sql.select([substr(dna.c.sequence,
t_loc.EnsemblStart,
length).label('sequence')],
dna.c.seq_region_id == t_loc.seq_region_id)
record = asserted_one(query.execute().fetchall())
seq = record['sequence']
seq = DNA.makeSequence(seq)
if t_loc.Strand == -1:
seq = seq.rc()
seqs.append(str(seq))
positions.append((q_loc.Start, q_loc.End))
sequence = _assemble_seq(seqs, coord.Start, coord.End, positions)
return sequence
def get_lower_coord_conversion(coord, species, core_db):
coord_system = CoordSystem(species=species, core_db=core_db)
seq_level_coord_type = CoordSystem(species=species,core_db=core_db,
seq_level=True)
query_rank = coord_system[coord.CoordType].rank
seq_level_rank = coord_system[seq_level_coord_type].rank
assemblies = None
for rank in range(query_rank+1, seq_level_rank):
coord_type = None
for key in coord_system.keys():
if coord_system[key].rank == rank:
coord_type = coord_system[key].name
break
if coord_type is None:
continue
assemblies = get_coord_conversion(coord, coord_type, core_db)
if assemblies:
break
return assemblies
def get_lower_coord_conversion(coord, species, core_db):
coord_system = CoordSystem(species=species, core_db=core_db)
seq_level_coord_type = CoordSystem(species=species,
core_db=core_db,
seq_level=True)
query_rank = coord_system[coord.CoordType].rank
seq_level_rank = coord_system[seq_level_coord_type].rank
assemblies = None
for rank in range(query_rank + 1, seq_level_rank):
coord_type = None
for key in coord_system.keys():
if coord_system[key].rank == rank:
coord_type = coord_system[key].name
break
if coord_type is None:
continue
assemblies = get_coord_conversion(coord, coord_type, core_db)
if assemblies:
break
return assemblies
