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# Copyright 2015-2017 by Kai Blin. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests Bio.SeqFeature.
"""
import unittest
from os import path
from Bio import SeqIO
from Bio.SeqFeature import FeatureLocation, AfterPosition, BeforePosition
from Bio.SeqFeature import CompoundLocation, UnknownPosition
class TestReference(unittest.TestCase):
"""Tests for the SeqFeature.Reference class"""
def test_eq_identical(self):
"""Test two identical references eq() to True"""
testfile = path.join('GenBank', 'origin_line.gb')
rec1 = SeqIO.read(testfile, 'genbank')
rec2 = SeqIO.read(testfile, 'genbank')
self.assertEqual(rec1.annotations['references'][0], rec1.annotations['references'][0])
cmp1, cmp2 = rec1.annotations['references'][0], rec2.annotations['references'][0]
self.assertEqual(cmp1, cmp2)
self.assertNotEqual(rec1.annotations['references'][0], rec1.annotations['references'][1])
self.assertNotEqual(rec1.annotations['references'][0], rec2.annotations['references'][1])
self.assertEqual(rec1.annotations['references'][1], rec1.annotations['references'][1])
self.assertEqual(rec1.annotations['references'][1], rec2.annotations['references'][1])
class TestFeatureLocation(unittest.TestCase):
"""Tests for the SeqFeature.FeatureLocation class"""
def test_eq_identical(self):
"""Test two identical locations are equal"""
loc1 = FeatureLocation(23, 42, 1)
loc2 = FeatureLocation(23, 42, 1)
self.assertEqual(loc1, loc2)
loc1 = FeatureLocation(23, 42, -1)
loc2 = FeatureLocation(23, 42, -1)
self.assertEqual(loc1, loc2)
loc1 = FeatureLocation(BeforePosition(23), AfterPosition(42), 1)
loc2 = FeatureLocation(23, 42, 1)
self.assertEqual(loc1, loc2)
loc1 = FeatureLocation(23, 42, 1, 'foo', 'bar')
loc2 = FeatureLocation(23, 42, 1, 'foo', 'bar')
self.assertEqual(loc1, loc2)
def test_eq_not_identical(self):
"""Test two different locations are not equal"""
loc1 = FeatureLocation(22, 42, 1)
loc2 = FeatureLocation(23, 42, 1)
self.assertNotEqual(loc1, loc2)
loc1 = FeatureLocation(23, 42, 1)
loc2 = FeatureLocation(23, 43, 1)
self.assertNotEqual(loc1, loc2)
loc1 = FeatureLocation(23, 42, 1)
loc2 = FeatureLocation(23, 42, -1)
self.assertNotEqual(loc1, loc2)
loc1 = FeatureLocation(23, 42, 1)
loc2 = (23, 42, 1)
self.assertNotEqual(loc1, loc2)
loc1 = FeatureLocation(23, 42, 1, 'foo')
loc2 = FeatureLocation(23, 42, 1, 'bar')
self.assertNotEqual(loc1, loc2)
loc1 = FeatureLocation(23, 42, 1, 'foo', 'bar')
loc2 = FeatureLocation(23, 42, 1, 'foo', 'baz')
self.assertNotEqual(loc1, loc2)
def test_start_before_end(self):
expected = "must be greater than or equal to start location"
with self.assertRaises(ValueError) as err:
FeatureLocation(42, 23, 1)
assert expected in str(err.exception)
with self.assertRaises(ValueError) as err:
FeatureLocation(42, 0, 1)
assert expected in str(err.exception)
with self.assertRaises(ValueError) as err:
FeatureLocation(BeforePosition(42), AfterPosition(23), -1)
assert expected in str(err.exception)
with self.assertRaises(ValueError) as err:
FeatureLocation(42, AfterPosition(0), 1)
assert expected in str(err.exception)
# Features with UnknownPositions should pass check
FeatureLocation(42, UnknownPosition())
FeatureLocation(UnknownPosition(), 42)
# Same start and end should pass check
FeatureLocation(42, 42)
class TestCompoundLocation(unittest.TestCase):
"""Tests for the SeqFeature.CompoundLocation class"""
def test_eq_identical(self):
"""Test two identical locations are equal"""
loc1 = FeatureLocation(12, 17, 1) + FeatureLocation(23, 42, 1)
loc2 = FeatureLocation(12, 17, 1) + FeatureLocation(23, 42, 1)
self.assertEqual(loc1, loc2)
loc1 = FeatureLocation(12, 17, 1) + FeatureLocation(23, 42, 1)
loc2 = CompoundLocation([FeatureLocation(12, 17, 1), FeatureLocation(23, 42, 1)])
self.assertEqual(loc1, loc2)
def test_eq_not_identical(self):
"""Test two different locations are not equal"""
loc1 = FeatureLocation(12, 17, 1) + FeatureLocation(23, 42, 1)
loc2 = FeatureLocation(12, 17, 1) + FeatureLocation(23, 42, 1) + FeatureLocation(50, 60, 1)
self.assertNotEqual(loc1, loc2)
loc1 = FeatureLocation(12, 17, 1) + FeatureLocation(23, 42, 1)
loc2 = FeatureLocation(12, 17, -1) + FeatureLocation(23, 42, -1)
self.assertNotEqual(loc1, loc2)
loc1 = CompoundLocation([FeatureLocation(12, 17, 1), FeatureLocation(23, 42, 1)])
loc2 = CompoundLocation([FeatureLocation(12, 17, 1), FeatureLocation(23, 42, 1)], 'order')
self.assertNotEqual(loc1, loc2)
loc1 = FeatureLocation(12, 17, 1) + FeatureLocation(23, 42, 1)
loc2 = 5
self.assertNotEqual(loc1, loc2)
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