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# Copyright (c) 2014-2016 Genome Research Ltd.
#
# This file is part of IVA.
#
# IVA is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 3 of the License, or (at your option) any later
# version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import filecmp
import pysam
from iva import graph, assembly, edge
from pyfastaq import intervals
modules_dir = os.path.dirname(os.path.abspath(graph.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')
class TestGraph(unittest.TestCase):
def setUp(self):
self.asm = assembly.Assembly(contigs_file=os.path.join(data_dir, 'graph_test.contigs.fa'))
self.g = graph.Graph(self.asm)
def test_get_nodes(self):
'''test get_nodes'''
self.assertListEqual(['c1', 'c2', 'c3', 'c4', 'c5', 'c6'], self.g.get_nodes())
def test_remove_node(self):
'''test remove_node'''
# TODO
pass
def test_add_and_get_edges(self):
'''test adding and getting edges'''
self.assertListEqual([], self.g._get_edges('not_in_graph', 'c1'))
self.assertListEqual([], self.g._get_edges('not_in_graph', 'c2'))
self.assertListEqual([], self.g._get_edges('c1', 'c2'))
self.assertListEqual([], self.g._get_edges('c2', 'c1'))
e1 = edge.Edge('c1', 1, 42, 'c2', 50, 10)
e2 = edge.Edge('c1', 4, 43, 'c2', 60, 10)
self.g.add_edge(e1)
self.assertListEqual([e1], self.g._get_edges('c1', 'c2'))
self.g.add_edge(e2)
self.assertListEqual([e1, e2], self.g._get_edges('c1', 'c2'))
with self.assertRaises(graph.Error):
self.g.add_edge(edge.Edge('c7', 1, 10, 'c8', 42, 84))
def test_degree(self):
'''test degree'''
self.assertEqual(0, self.g._degree('c1'))
self.assertEqual(0, self.g._degree('c2'))
e1 = edge.Edge('c1', 1, 42, 'c2', 50, 10)
e2 = edge.Edge('c1', 4, 43, 'c2', 60, 10)
self.g.add_edge(e1)
self.assertEqual(1, self.g._degree('c1'))
self.assertEqual(1, self.g._degree('c2'))
self.g.add_edge(e2)
self.assertEqual(2, self.g._degree('c1'))
self.assertEqual(2, self.g._degree('c2'))
def test_connected_components(self):
'''test connected_components'''
self.assertListEqual([['c1'], ['c2'], ['c3'], ['c4'], ['c5'], ['c6']], self.g.connected_components())
self.g.add_edge(edge.Edge('c1', 42, 1, 'c2', 1, 10))
self.assertListEqual([['c1', 'c2'], ['c3'], ['c4'], ['c5'], ['c6']], self.g.connected_components())
self.g.add_edge(edge.Edge('c3', 42, 1, 'c2', 1, 10))
self.assertListEqual([['c1', 'c2', 'c3'], ['c4'], ['c5'], ['c6']], self.g.connected_components())
def test_find_simple_path(self):
'''test find_simple_path'''
self.assertListEqual([], self.g.find_simple_path(['c1']))
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.assertListEqual(['c1', 'c2'], self.g.find_simple_path(['c1', 'c2']))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertListEqual(['c1', 'c2', 'c3'], self.g.find_simple_path(['c1', 'c2', 'c3']))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertListEqual([], self.g.find_simple_path(['c1', 'c2', 'c3']))
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.assertListEqual([], self.g.find_simple_path(['c1', 'c2']))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.g.add_edge(edge.Edge('c3', 10, 100, 'c4', 1, 1000))
self.assertListEqual(['c1', 'c2', 'c3', 'c4'], self.g.find_simple_path(['c1', 'c2', 'c3', 'c4']))
self.g.add_edge(edge.Edge('c3', 10, 100, 'c5', 1, 1000))
self.assertListEqual([], self.g.find_simple_path(['c1', 'c2', 'c3']))
def test_remove_middle_node(self):
'''test remove_middle_node'''
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 100, 142, 'c3', 1, 42))
self.assertFalse(self.g._remove_middle_node('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 51, 100, 'c2', 1, 50))
self.g.add_edge(edge.Edge('c2', 41, 80, 'c3', 1, 40))
self.assertTrue(self.g._remove_middle_node('c1', 'c2', 'c3'))
self.assertTrue('c2' not in self.g.graph)
self.assertEqual(1, len(self.g.graph['c1']['c3']['edges']))
self.assertEqual(1, len(self.g.graph['c3']['c1']['edges']))
self.assertEqual(self.g.graph['c1']['c3']['edges'][0], edge.Edge('c1', 91, 100, 'c3', 1, 10))
self.assertEqual(self.g.graph['c3']['c1']['edges'][0], edge.Edge('c1', 91, 100, 'c3', 1, 10))
def test_remove_redundant_nodes_from_simple_path(self):
'''test remove_redundant_nodes_from_simple_path'''
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 100, 142, 'c3', 1, 42))
new_path = self.g.remove_redundant_nodes_from_simple_path(['c1', 'c2', 'c3'])
self.assertListEqual(['c1', 'c2', 'c3'], new_path)
self.assertTrue('c2' in self.g.graph)
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 51, 100, 'c2', 1, 50))
self.g.add_edge(edge.Edge('c2', 41, 80, 'c3', 1, 40))
new_path = self.g.remove_redundant_nodes_from_simple_path(['c1', 'c2', 'c3'])
self.assertListEqual(['c1', 'c3'], new_path)
self.assertFalse('c2' in self.g.graph)
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 51, 100, 'c2', 1, 50))
self.g.add_edge(edge.Edge('c2', 41, 80, 'c3', 1, 40))
self.g.add_edge(edge.Edge('c3', 100, 150, 'c4', 1, 50))
self.g.add_edge(edge.Edge('c4', 20, 70, 'c5', 1, 50))
self.g.add_edge(edge.Edge('c5', 40, 90, 'c6', 1, 50))
new_path = self.g.remove_redundant_nodes_from_simple_path(['c1', 'c2', 'c3', 'c4', 'c5', 'c6'])
self.assertListEqual(['c1', 'c3', 'c5', 'c6'], new_path)
self.assertFalse('c2' in self.g.graph)
self.assertFalse('c4' in self.g.graph)
def test_node_to_coords(self):
'''test _node_to_coords'''
self.g.add_edge(edge.Edge('c1', 199, 0, 'c2', 1319, 1119))
nodes = ['c1', 'c2']
self.assertListEqual(['c1', intervals.Interval(200, 659), True], self.g._node_to_coords(nodes, 0))
self.assertListEqual(['c2', intervals.Interval(0, 1319), True], self.g._node_to_coords(nodes, 1))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c2', 1119, 1319, 'c1', 0, 199))
nodes = ['c1', 'c2']
self.assertListEqual(['c1', intervals.Interval(200, 659), True], self.g._node_to_coords(nodes, 0))
self.assertListEqual(['c2', intervals.Interval(0, 1319), True], self.g._node_to_coords(nodes, 1))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 551, 650, 'c2', 1, 100))
self.g.add_edge(edge.Edge('c2', 1201, 1300, 'c3', 11, 110))
nodes = ['c1', 'c2', 'c3']
self.assertListEqual(['c1', intervals.Interval(0, 550), False], self.g._node_to_coords(nodes, 0))
self.assertListEqual(['c2', intervals.Interval(1, 1200), False], self.g._node_to_coords(nodes, 1))
self.assertListEqual(['c3', intervals.Interval(11, 2159), False], self.g._node_to_coords(nodes, 2))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 551, 650, 'c2', 1, 100))
self.g.add_edge(edge.Edge('c3', 110, 11, 'c2', 1300, 1201))
self.g.add_edge(edge.Edge('c3', 2051, 2150, 'c4', 6, 115))
nodes = ['c1', 'c2', 'c3', 'c4']
self.assertListEqual(['c1', intervals.Interval(0, 550), False], self.g._node_to_coords(nodes, 0))
self.assertListEqual(['c2', intervals.Interval(1, 1200), False], self.g._node_to_coords(nodes, 1))
self.assertListEqual(['c3', intervals.Interval(11, 2050), False], self.g._node_to_coords(nodes, 2))
self.assertListEqual(['c4', intervals.Interval(6, 1259), False], self.g._node_to_coords(nodes, 3))
def test_merged_coords_from_simple_nonredundant_path(self):
'''test merged_coords_from_simple_nonredundant_path'''
self.g.add_edge(edge.Edge('c1', 199, 0, 'c2', 1319, 1119))
nodes = ['c1', 'c2']
coords = self.g.merged_coords_from_simple_nonredundant_path(nodes)
expected = [
['c1', intervals.Interval(200, 659), True],
['c2', intervals.Interval(0, 1319), True],
]
self.assertListEqual(expected, coords)
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 610, 652, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 1250, 1310, 'c3', 5, 65))
nodes = ['c1', 'c2', 'c3']
coords = self.g.merged_coords_from_simple_nonredundant_path(nodes)
expected = [
['c1', intervals.Interval(0, 609), False],
['c2', intervals.Interval(1, 1249), False],
['c3', intervals.Interval(5, 2159), False]
]
self.assertListEqual(expected, coords)
def test_simple_path_is_consistent(self):
'''test simple_path_is_consistent'''
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertTrue(self.g.simple_path_is_consistent(['c1', 'c2']))
self.g.add_edge(edge.Edge('c3', 10, 100, 'c4', 1, 1000))
self.assertTrue(self.g.simple_path_is_consistent(['c1', 'c2', 'c3']))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 1000, 100, 'c3', 1, 42))
self.assertFalse(self.g.simple_path_is_consistent(['c1', 'c2', 'c3']))
def test_edges_are_consistent(self):
'''test edges_are_consistent'''
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertTrue(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g.add_edge(edge.Edge('c1', 1, 100, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 100, 50, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 42, 1))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
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