def test_add_multiple_transformations():
"""We expect that when we add a record with a transformation, that the we
can obtain the origin record and transformed record."""
db = SeqRecordDB()
from uuid import uuid4
from pyblast.constants import Constants as C
def pseudocircularize(r):
pseudor = r + r
pseudor.name = C.PSEUDOCIRCULAR + "__" + r.name
pseudor.id = str(uuid4())
return pseudor
record = SeqRecord(
Seq("ACGTTCGTGATTGTGCTGTGTGTATGGTATGATTATAGTGATGTAGTGATGATGTAGTAGTATA")
)
r1 = deepcopy(record)
r2 = deepcopy(record)
r1.id = "record1"
r2.id = "record2"
records = make_circular([r1, r2])
keys = db.add_many_with_transformations(records, pseudocircularize,
C.PSEUDOCIRCULAR)
assert len(keys) == 2
assert len(db) == 4
def test_add_with_transform():
"""We expect that when we add a record with a transformation, that the we
can obtain the origin record and transformed record."""
db = SeqRecordDB()
from uuid import uuid4
from pyblast.constants import Constants as C
def pseudocircularize(r):
r2 = r + r
r2.name = C.PSEUDOCIRCULAR + "__" + r.name
r2.id = str(uuid4())
return r2
record = SeqRecord(
Seq("ACGTTCGTGATTGTGCTGTGTGTATGGTATGATTATAGTGATGTAGTGATGATGTAGTAGTATA")
)
records = make_circular([record])
keys = db.add_many_with_transformations(records, pseudocircularize,
C.PSEUDOCIRCULAR)
key = keys[0]
origin_key = db.get_origin_key(key)
origin = db.get_origin(key)
transformed = db.get(key)
assert origin is record
assert origin is not transformed
assert origin_key is not key
assert len(transformed) == 2 * len(record)
def test_add_same_transformation():
"""We expect that when we add a record with a transformation, that the we
can obtain the origin record and transformed record."""
db = SeqRecordDB()
from uuid import uuid4
from pyblast.constants import Constants as C
def pseudocircularize(r):
r2 = r + r
r2.name = C.PSEUDOCIRCULAR + "__" + r.name
r2.id = str(uuid4())
return r2
record = SeqRecord(
Seq("ACGTTCGTGATTGTGCTGTGTGTATGGTATGATTATAGTGATGTAGTGATGATGTAGTAGTATA")
)
records = make_circular([record, record])
keys = db.add_many_with_transformations(records, pseudocircularize,
C.PSEUDOCIRCULAR)
assert len(set(keys)) == 1
assert len(db) == 2
def __init__(self, seq_db=None, span_origin=True, config=None):
"""Initialize a new BioBlastFactory.
:param seq_db: the optional SeqRecordDB. If not provided, a new one will be
created.
:type seq_db: SeqRecordDB
"""
if seq_db is None:
self.db = SeqRecordDB()
else:
self.db = seq_db
self.span_origin = span_origin
self.record_groups = {}
self.logger = logger(self)
self.config = config
def test_get_records():
db = SeqRecordDB()
keys = db.add_many([random_record(), random_record()])
assert keys
assert db.get_many(keys)
def test_get_record():
db = SeqRecordDB()
r = random_record()
k = db.add(r)
assert k
assert db.get(k) is r
def test_add_records():
db = SeqRecordDB()
db.add_many([random_record(), random_record()])
def test_add_record():
db = SeqRecordDB()
db.add(random_record())
def test_init():
SeqRecordDB()