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 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_oneof(self):
"""Features: write/read simple one-of locations."""
start = OneOfPosition(
[ExactPosition(0),
ExactPosition(3),
ExactPosition(6)])
f = SeqFeature(FeatureLocation(start, 21), strand=+1, type="CDS")
self.assertEqual(_insdc_feature_location_string(f),
"one-of(1,4,7)..21")
self.record.features.append(f)
start = OneOfPosition([ExactPosition(x) for x in [10, 13, 16]])
end = OneOfPosition([ExactPosition(x) for x in [41, 44, 50]])
f = SeqFeature(FeatureLocation(start, end), strand=+1, type="gene")
self.assertEqual(_insdc_feature_location_string(f),
"one-of(11,14,17)..one-of(41,44,50)")
self.record.features.append(f)
end = OneOfPosition([ExactPosition(x) for x in [30, 33]])
f = SeqFeature(FeatureLocation(27, end), strand=+1, type="gene")
self.assertEqual(_insdc_feature_location_string(f),
"28..one-of(30,33)")
self.record.features.append(f)
start = OneOfPosition([ExactPosition(x) for x in [36, 40]])
f = SeqFeature(FeatureLocation(start, 46), strand=-1, type="CDS")
self.assertEqual(_insdc_feature_location_string(f),
"complement(one-of(37,41)..46)")
self.record.features.append(f)
start = OneOfPosition([ExactPosition(x) for x in [45, 60]])
end = OneOfPosition([ExactPosition(x) for x in [70, 90]])
f = SeqFeature(FeatureLocation(start, end), strand=-1, type="CDS")
self.assertEqual(_insdc_feature_location_string(f),
"complement(one-of(46,61)..one-of(70,90))")
self.record.features.append(f)
end = OneOfPosition([ExactPosition(x) for x in [60, 63]])
f = SeqFeature(FeatureLocation(55, end), strand=-1, type="tRNA")
self.assertEqual(_insdc_feature_location_string(f),
"complement(56..one-of(60,63))")
self.record.features.append(f)
self.write_read_check()