def test_pickle(self):
"""Test pickle behaviour of position instances."""
# setup
import pickle
within_pos = WithinPosition(10, left=10, right=13)
between_pos = BetweenPosition(24, left=20, right=24)
oneof_pos = OneOfPosition(
1888,
[ExactPosition(1888), ExactPosition(1901)])
# test __getnewargs__
self.assertEqual(within_pos.__getnewargs__(), (10, 10, 13))
self.assertEqual(between_pos.__getnewargs__(), (24, 20, 24))
self.assertEqual(
oneof_pos.__getnewargs__(),
(1888, [ExactPosition(1888),
ExactPosition(1901)]),
)
# test pickle behaviour
within_pos2 = pickle.loads(pickle.dumps(within_pos))
between_pos2 = pickle.loads(pickle.dumps(between_pos))
oneof_pos2 = pickle.loads(pickle.dumps(oneof_pos))
self.assertEqual(within_pos, within_pos2)
self.assertEqual(between_pos, between_pos2)
self.assertEqual(oneof_pos, oneof_pos2)
self.assertEqual(within_pos._left, within_pos2._left)
self.assertEqual(within_pos._right, within_pos2._right)
self.assertEqual(between_pos._left, between_pos2._left)
self.assertEqual(between_pos._right, between_pos2._right)
self.assertEqual(oneof_pos.position_choices,
oneof_pos2.position_choices)
def test_within(self):
"""Features: write/read simple within locations."""
f = SeqFeature(FeatureLocation(WithinPosition(2,6),10), \
strand=+1, type="CDS")
self.assertEqual(_insdc_feature_location_string(f), "(3.9)..10")
self.record.features.append(f)
f = SeqFeature(FeatureLocation(WithinPosition(12,6),
WithinPosition(20,8)), \
strand=+1, type="CDS")
self.assertEqual(_insdc_feature_location_string(f), "(13.19)..(20.28)")
self.record.features.append(f)
f = SeqFeature(FeatureLocation(25,WithinPosition(30,3)), \
strand=+1, type="misc_feature")
self.assertEqual(_insdc_feature_location_string(f), "26..(30.33)")
self.record.features.append(f)
f = SeqFeature(FeatureLocation(WithinPosition(35,4),40), \
strand=-1, type="rRNA")
self.assertEqual(_insdc_feature_location_string(f),
"complement((36.40)..40)")
self.record.features.append(f)
f = SeqFeature(FeatureLocation(WithinPosition(45,2),
WithinPosition(50,3)), \
strand=-1, type="repeat_region")
self.assertEqual(_insdc_feature_location_string(f),
"complement((46.48)..(50.53))")
self.record.features.append(f)
f = SeqFeature(FeatureLocation(55,WithinPosition(60,5)), \
strand=-1, type="CDS")
self.assertEqual(_insdc_feature_location_string(f),
"complement(56..(60.65))")
self.record.features.append(f)
self.write_read_check()
def setUp(self):
f0 = SeqFeature(
FeatureLocation(0, 26),
type="source",
qualifiers={"mol_type": ["fake protein"]},
)
f1 = SeqFeature(FeatureLocation(0, ExactPosition(10)))
f2 = SeqFeature(
FeatureLocation(WithinPosition(12, left=12, right=15),
BeforePosition(22)))
f3 = SeqFeature(
FeatureLocation(
AfterPosition(16),
OneOfPosition(
26,
[ExactPosition(25), AfterPosition(26)]),
))
self.record = SeqRecord(
Seq("ABCDEFGHIJKLMNOPQRSTUVWZYX", generic_protein),
id="TestID",
name="TestName",
description="TestDescr",
dbxrefs=["TestXRef"],
annotations={"k": "v"},
letter_annotations={"fake": "X" * 26},
features=[f0, f1, f2, f3],
)
def test_fuzzy_join(self):
"""Features: write/read fuzzy join locations."""
f1 = SeqFeature(FeatureLocation(BeforePosition(10), 20), strand=+1)
f2 = SeqFeature(FeatureLocation(25, AfterPosition(40)), strand=+1)
f = self.make_join_feature([f1, f2])
self.record.features.append(f)
self.assertEqual(_insdc_feature_location_string(f),
"join(<11..20,26..>40)")
f1 = SeqFeature(FeatureLocation(
OneOfPosition([ExactPosition(107),
ExactPosition(110)]), 120),
strand=+1)
f2 = SeqFeature(FeatureLocation(125, 140), strand=+1)
f3 = SeqFeature(FeatureLocation(145, WithinPosition(150, 10)),
strand=+1)
f = self.make_join_feature([f1, f2, f3], "CDS")
self.assertEqual(_insdc_feature_location_string(f),
"join(one-of(108,111)..120,126..140,146..(150.160))")
self.record.features.append(f)
f1 = SeqFeature(FeatureLocation(BeforePosition(210), 220), strand=-1)
f2 = SeqFeature(FeatureLocation(225, WithinPosition(240, 4)),
strand=-1)
f = self.make_join_feature([f1, f2], "gene")
self.assertEqual(_insdc_feature_location_string(f),
"complement(join(<211..220,226..(240.244)))")
self.record.features.append(f)
f1 = SeqFeature(FeatureLocation(AfterPosition(310), 320), strand=-1)
f2 = SeqFeature(FeatureLocation(
325, OneOfPosition([ExactPosition(340),
ExactPosition(337)])),
strand=-1)
f3 = SeqFeature(FeatureLocation(345, WithinPosition(350, 5)),
strand=-1)
f = self.make_join_feature([f1, f2, f3], "CDS")
self.assertEqual(
_insdc_feature_location_string(f),
"complement(join(>311..320,326..one-of(340,337),346..(350.355)))")
self.record.features.append(f)
self.write_read_check()
def test_fuzzy(self):
"""Test fuzzy representations."""
# check the positions alone
exact_pos = ExactPosition(5)
within_pos_s = WithinPosition(10, left=10, right=13)
within_pos_e = WithinPosition(13, left=10, right=13)
between_pos_e = BetweenPosition(24, left=20, right=24)
before_pos = BeforePosition(15)
after_pos = AfterPosition(40)
self.assertEqual(int(within_pos_s), 10)
self.assertEqual(str(within_pos_s), "(10.13)")
self.assertEqual(int(within_pos_e), 13)
self.assertEqual(str(within_pos_e), "(10.13)")
self.assertEqual(int(between_pos_e), 24)
self.assertEqual(str(between_pos_e), "(20^24)")
self.assertEqual(str(before_pos), "<15")
self.assertEqual(str(after_pos), ">40")
# put these into Locations
location1 = FeatureLocation(exact_pos, within_pos_e)
location2 = FeatureLocation(before_pos, between_pos_e)
location3 = FeatureLocation(within_pos_s, after_pos)
self.assertEqual(str(location1), "[5:(10.13)]")
self.assertEqual(str(location1.start), "5")
self.assertEqual(str(location1.end), "(10.13)")
self.assertEqual(str(location2), "[<15:(20^24)]")
self.assertEqual(str(location2.start), "<15")
self.assertEqual(str(location2.end), "(20^24)")
self.assertEqual(str(location3), "[(10.13):>40]")
self.assertEqual(str(location3.start), "(10.13)")
self.assertEqual(str(location3.end), ">40")
# --- test non-fuzzy representations
self.assertEqual(location1.nofuzzy_start, 5)
self.assertEqual(location1.nofuzzy_end, 13)
self.assertEqual(location2.nofuzzy_start, 15)
self.assertEqual(location2.nofuzzy_end, 24)
self.assertEqual(location3.nofuzzy_start, 10)
self.assertEqual(location3.nofuzzy_end, 40)