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from __future__ import absolute_import, unicode_literals
import pytest
pygr = pytest.importorskip("pygr")
import screed # nopep8
from screed.DBConstants import fileExtension # nopep8
from screed.pygr_api import ScreedSequenceDB, ScreedSequenceDB_ByIndex # nopep8
from pickle import dump, load # nopep8
from io import StringIO # nopep8
import os # nopep8
testfa = os.path.join(os.path.dirname(__file__), 'test.fa')
def setup():
screed.read_fasta_sequences(testfa)
def teardown():
os.unlink(testfa + fileExtension)
def test_name_iterator_methods():
db = ScreedSequenceDB(testfa)
# test the various iterator methods for equal results from db
a = sorted([(x, db[x]) for x in db])
b = sorted([i for i in db.iteritems()])
c = sorted([(v.name, v) for v in db.itervalues()])
assert a == b
assert a == c
def test_index_iterator_methods():
db = ScreedSequenceDB_ByIndex(testfa)
# test the various iterator methods for equal results from db
m = sorted([(x, db[x]) for x in db])
n = sorted([i for i in db.iteritems()])
o = sorted([(v.record.id, v) for v in db.itervalues()])
assert m == n
assert m == o, (m, o)
def test_name_index_equality():
db1 = ScreedSequenceDB(testfa)
db2 = ScreedSequenceDB_ByIndex(testfa)
# must use something other than the obj itself for comparison...
v1 = sorted([(v.name, v.seq) for v in db1.itervalues()])
v2 = sorted([(v.name, v.seq) for v in db2.itervalues()])
assert v1 == v2, (v1, v2)
def test_seqinfodict_by_name():
db1 = ScreedSequenceDB(testfa)
sd = db1.seqInfoDict
m = sorted([y.id for (x, y) in sd.iteritems()])
n = sorted([x.id for x in sd.itervalues()])
assert m == n, (m, n)
def test_seqinfodict_by_index():
db1 = ScreedSequenceDB_ByIndex(testfa)
sd = db1.seqInfoDict
m = sorted([x for (x, y) in sd.iteritems()])
n = sorted([x for x in sd.iterkeys()])
assert m == n, (m, n)
def test_pickle_ByName():
db = ScreedSequenceDB(testfa)
ofp = StringIO()
dump(db, ofp)
ifp = StringIO(ofp.getvalue())
db2 = load(ifp)
assert db.filepath == db2.filepath
def test_pickle_ByIndex():
db = ScreedSequenceDB_ByIndex(testfa)
ofp = StringIO()
dump(db, ofp)
ifp = StringIO(ofp.getvalue())
db2 = load(ifp)
assert db.filepath == db2.filepath
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