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unitTest_Alignment.py
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unitTest_Alignment.py
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import unittest
from gengraphTool import *
import networkx as nx
import matplotlib.pyplot as plt
from gengraph import *
import networkx.algorithms.isomorphism as iso
# - No mutations, all sequences the same, only one node
# - One mutation in one of the strains, a single substitution.
# - Same for a single deletion
# - And an insertion
# - A large rearrangement where 300bp are reverse complimented in one sequence.
# - A large rearrangement where 300bp are reverse complimented in one sequence containing a SNP in the reversed sequence.
# - One with a general mix of SNPS
# TO run a specific test: python3 -m unittest -v unitTest_Alignment.MultipleSequenceAlignmentTest.align_one_read
# To profile do: python3 -m cProfile -o gengraphTool_6genome.prof ./gengraphTool.py make_genome_graph --seq_file ./test_files/multiGenome6.txt --out_file_name test6genome
test_graph_dir = './TestGraphs/'
class BasicTests(unittest.TestCase):
noMutationRead = "GCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGA"
noMutationGraph = import_gg_graph(test_graph_dir + 'no_mutation.xml')
def test_read_Length(self):
self.assertEqual(readLength(self.noMutationRead), 100)
def test_sequence_Length(self):
self.assertEqual(sequenceLength(self.noMutationGraph), 1000)
def test_no_of_Isolates(self):
self.assertEqual(isolateNumber(self.noMutationGraph), 3)
class NoMutationsTests(unittest.TestCase):
noMutationRead = "GCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGA"
noMutationGraph = import_gg_graph(test_graph_dir + 'no_mutation.xml')
def test_no_of_nodes(self):
self.assertEqual(nodeNumber(self.noMutationGraph), 1)
def test_nodes_covered_by_read(self):
self.assertEqual(coverage(self.noMutationGraph, self.noMutationRead), 1)
def test_alignment_Start(self):
self.assertEqual(alignStartPosition(self.noMutationGraph, self.noMutationRead), 100)
def test_alignment_End(self):
self.assertEqual(alignEndPosition(self.noMutationGraph, self.noMutationRead), 199)
def test_coverage_Percentage(self):
self.assertEqual(coverage(self.noMutationGraph, self.noMutationRead), "10%")
def test_query_alignment_Percentage(self):
self.assertEqual(queryAlignmentPercentage(self.noMutationGraph, self.noMutationRead), "100%")
class OneSubstitutionTest(unittest.TestCase):
oneSubstitutionGraph = import_gg_graph(test_graph_dir + 'one_sub.xml')
readWithSubstitution = "CACAGTGTGGCACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAG"
readWithoutSubstitution = "CACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAG"
def test_no_of_nodes(self):
self.assertEqual(nodeNumber(self.oneSubstitutionGraph), 4)
def test_nodes_covered_by_read(self):
self.assertEqual(coverage(self.oneSubstitutionGraph, self.readWithoutSubstitution), 3)
self.assertEqual(coverage(self.oneSubstitutionGraph, self.readWithSubstitution), 3)
def test_alignment_Start(self):
self.assertEqual(alignStartPosition(self.oneSubstitutionGraph, self.readWithoutSubstitution), 30)
def test_alignment_End(self):
self.assertEqual(alignEndPosition(self.oneSubstitutionGraph, self.readWithoutSubstitution), 129)
def test_coverage_Percentage(self):
self.assertEqual(coverage(self.oneSubstitutionGraph, self.readWithoutSubstitution), "10%")
self.assertEqual(coverage(self.oneSubstitutionGraph, self.readWithSubstitution), "10%")
def test_query_alignment_Percentage(self):
self.assertEqual(queryAlignmentPercentage(self.oneSubstitutionGraph, self.readWithoutSubstitution), "100%")
self.assertEqual(queryAlignmentPercentage(self.oneSubstitutionGraph, self.readWithSubstitution), "100%")
def test_sequence_Differences(self):
self.assertEqual(isolateSequenceDifferences(self.oneSubstitutionGraph.get_sequence(0, 999, 'H37Rv'), self.oneSubstitutionGraph.get_sequence(0, 999, 'H37Rv_2')), 0)
self.assertEqual(isolateSequenceDifferences(self.oneSubstitutionGraph.get_sequence(0, 999, 'H37Rv'), self.oneSubstitutionGraph.get_sequence(0, 999, 'H37Rv_One_Sub')), 1)
self.assertEqual(isolateSequenceDifferences(self.oneSubstitutionGraph.get_sequence(0, 999, 'H37Rv_2'), self.oneSubstitutionGraph.get_sequence(0, 999, 'H37Rv_One_Sub')), 1)
class OneDeletionTest(unittest.TestCase):
oneDeletionGraph = import_gg_graph(test_graph_dir + 'one_deletion.xml')
readWithDeletion = "CACAGTGTGGAACGCGGTCGCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGC"
readWithoutDeletion = "CACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAG"
def test_no_of_nodes(self):
self.assertEqual(nodeNumber(self.oneDeletionGraph), 3)
def test_nodes_covered_by_read(self):
self.assertEqual(coverage(self.oneDeletionGraph, self.readWithoutDeletion), 3)
self.assertEqual(coverage(self.oneDeletionGraph, self.readWithDeletion), 3)
def test_alignment_Start(self):
self.assertEqual(alignStartPosition(self.oneDeletionGraph, self.readWithoutDeletion), 30)
def test_alignment_End(self):
self.assertEqual(alignEndPosition(self.oneDeletionGraph, self.readWithoutDeletion), 129)
def test_coverage_Percentage(self):
self.assertEqual(coverage(self.oneDeletionGraph, self.readWithoutDeletiond), "10%")
self.assertEqual(coverage(self.oneDeletionGraph, self.readWithDeletion), "10%")
def test_query_alignment_Percentage(self):
self.assertEqual(queryAlignmentPercentage(self.oneDeletionGraph, self.readWithoutDeletion), "100%")
self.assertEqual(queryAlignmentPercentage(self.oneDeletionGraph, self.readWithDeletion), "10%")
def test_sequence_Differences(self):
self.assertEqual(isolateSequenceDifferences(self.oneDeletionGraph.get_sequence(0, 999, 'H37Rv'), self.oneDeletionGraph.get_sequence(0, 999, 'H37Rv_2')), 0)
self.assertEqual(isolateSequenceDifferences(self.oneDeletionGraph.get_sequence(0, 999, 'H37Rv'), self.oneDeletionGraph.get_sequence(0, 999, 'H37Rv_One_Deletion')), 1)
self.assertEqual(isolateSequenceDifferences(self.oneDeletionGraph.get_sequence(0, 999, 'H37Rv_2'), self.oneDeletionGraph.get_sequence(0, 999, 'H37Rv_One_Deletion')), 1)
class OneInsertionTest(unittest.TestCase):
oneInsertionGraph = import_gg_graph(test_graph_dir + 'one_insertion.xml')
readWithInsertion = "CACAGTGTGGAACGCGGTCGTCTCCGAACTTAGACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCA"
readWithoutInsertion = "CACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAG"
def test_no_of_nodes(self):
self.assertEqual(nodeNumber(self.oneInsertionGraph), 3)
def test_nodes_covered_by_read(self):
self.assertEqual(coverage(self.oneInsertionGraph, self.readWithoutInsertion), 2)
self.assertEqual(coverage(self.oneInsertionGraph, self.readWithInsertion), 3)
def test_alignment_Start(self):
self.assertEqual(alignStartPosition(self.oneInsertionGraph, self.readWithoutInsertion), 30)
def test_alignment_End(self):
self.assertEqual(alignEndPosition(self.oneInsertionGraph, self.readWithoutInsertion), 129)
def test_coverage_Percentage(self):
self.assertEqual(coverage(self.oneInsertionGraph, self.readWithoutInsertion), "10%")
self.assertEqual(coverage(self.oneInsertionGraph, self.readWithInsertion), "10%")
def test_query_alignment_Percentage(self):
self.assertEqual(queryAlignmentPercentage(self.oneInsertionGraph, self.readWithoutInsertion), "100%")
self.assertEqual(queryAlignmentPercentage(self.oneInsertionGraph, self.readWithInsertion), "100%")
def test_sequence_Differences(self):
self.assertEqual(isolateSequenceDifferences(self.oneInsertionGraph.get_sequence(0, 999, 'H37Rv'), self.oneInsertionGraph.get_sequence(0, 999, 'H37Rv_2')), 0)
self.assertEqual(isolateSequenceDifferences(self.oneInsertionGraph.get_sequence(0, 999, 'H37Rv'), self.oneInsertionGraph.get_sequence(0, 999, 'H37Rv_One_Deletion')), 1)
self.assertEqual(isolateSequenceDifferences(self.oneInsertionGraph.get_sequence(0, 999, 'H37Rv_2'), self.oneInsertionGraph.get_sequence(0, 999, 'H37Rv_One_Deletion')), 1)
'''
class ReverseComplimentTest(unittest.TestCase):
reverseComplimentGraph = import_gg_graph(test_graph_dir + 'reverse.xml')
read = "TCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGGTTAGAGCAGCAACAGCCAACACCACAGACCGCTACACCATCGTCCTAAA"
def test_no_of_nodes(self):
self.assertEqual(nodeNumber(self.reverseComplimentGraph), 245)
def test_nodes_covered_by_read(self):
self.assertEqual(coverage(self.reverseComplimentGraph, self.read), 29)
def test_alignment_Start(self):
self.assertEqual(alignStartPosition(self.reverseComplimentGraph, self.read), 50)
def test_alignment_End(self):
self.assertEqual(alignEndPosition(self.reverseComplimentGraph, self.read), 149)
def test_coverage_Percentage(self):
self.assertEqual(coverage(graphObject, read), "10%")
def test_query_alignment_Percentage(self):
self.assertEqual(queryAlignmentPercentage(self.reverseComplimentGraph, self.read), "100%")
def test_sequence_Differences(self):
self.assertEqual(isolateSequenceDifferences(seq1, seq2), 0)
self.assertEqual(isolateSequenceDifferences(seq1, seq3), 300)
self.assertEqual(isolateSequenceDifferences(seq2, seq3), 300)
def test_contain_reverse(self):
self.assertTrue(containReverse(self.reverseComplimentGraph))
class ReverseComplimentWithSNPTest(unittest.TestCase):
reverseComplimentGraph = import_gg_graph(test_graph_dir + 'reverse_with_snp.xml')
read = "TCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATTGTTAGAGCAGCAACAGCCAACACCACAGACCGCTACACCATCGTCCTAAA"
def test_no_of_nodes(self):
self.assertEqual(nodeNumber(self.reverseComplimentGraph), 245)
def test_nodes_covered_by_read(self):
self.assertEqual(coverage(self.reverseComplimentGraph, self.read), 29)
def test_alignment_Start(self):
self.assertEqual(alignStartPosition(self.reverseComplimentGraph, self.read), 50)
def test_alignment_End(self):
self.assertEqual(alignEndPosition(self.reverseComplimentGraph, self.read), 149)
def test_coverage_Percentage(self):
self.assertEqual(coverage(graphObject, read), "10%")
def test_query_alignment_Percentage(self):
self.assertEqual(queryAlignmentPercentage(self.reverseComplimentGraph, self.read), "100%")
def test_sequence_Differences(self):
self.assertEqual(isolateSequenceDifferences(seq1, seq2), 0)
self.assertEqual(isolateSequenceDifferences(seq1, seq3), 300)
self.assertEqual(isolateSequenceDifferences(seq2, seq3), 300)
def test_contain_reverse(self):
self.assertTrue(containReverse(self.reverseComplimentGraph))
'''
class MixOfSNPTest(unittest.TestCase):
mixOfSNPGraph = import_gg_graph(test_graph_dir + 'mix_of_snps.xml')
read = "TTGCCCGATGACCCCGGTTCAGGCTTCACCAGAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATG"
def test_no_of_nodes(self):
self.assertEqual(nodeNumber(self.mixOfSNPGraph), 19)
def test_nodes_covered_by_read(self):
self.assertEqual(coverage(self.mixOfSNPGraph, self.read), 5)
def test_alignment_Start(self):
self.assertEqual(alignStartPosition(self.mixOfSNPGraph, self.read), 0)
def test_alignment_End(self):
self.assertEqual(alignEndPosition(self.mixOfSNPGraph, self.read), 99)
def test_coverage_Percentage(self):
self.assertEqual(coverage(self.mixOfSNPGraph, self.read), "10%")
def test_query_alignment_Percentage(self):
self.assertEqual(queryAlignmentPercentage(self.mixOfSNPGraph, self.read), "100%")
def test_sequence_Differences(self):
self.assertEqual(isolateSequenceDifferences(seq1, seq2), 0)
self.assertEqual(isolateSequenceDifferences(seq1, seq3), 6)
self.assertEqual(isolateSequenceDifferences(seq2, seq3), 6)
def test_contain_reverse(self):
self.assertFalse(containReverse(self.mixOfSNPGraph))
def test_no_of_SNPS(self):
self.assertEqual(noOfSNPS(self.mixOfSNPGraph), 6)
def test_list_of_SNPS(self):
self.assertEqual(listOfSNPS(self.mixOfSNPGraph), ["A,C,4", "C,G,32", "C,A,118", "A,C,166", "C,G,240", "A,T,993"])
class GraphSimilarityTest(unittest.TestCase):
# Can remove section graph aligns to and insert the read, then check whether graphs are similar or the same
oneSubstitutionGraph = import_gg_graph(test_graph_dir + 'one_sub.xml')
readWithSubstitution = "CACAGTGTGGCACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAG"
readwithOneDifference = "CACAGTGTGGCACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGTGCTCCGCTGACCCCTCAG"
def test_isomorphism(self):
# changedGraph has matched read inserted to replace sequence it matches to
# if it is ismorphic then it proves that the read aligns perfectly to a section of the GenGraph
changedGraph = insertAlignedRead(self.oneSubstitutionGraph, self.readWithSubstitution)
self.assertTrue(isIsomorphic(self.oneSubstitutionGraph , changedGraph))
self.assertEqual(calculateGED(self.oneSubstitutionGraph, changedGraph), 0.0)
def test_GED(self):
# The graph edit distance is the number of changes to nodes/edges to make two graphs isomorphic(identical)
# This can show how similar two graphs are and how well the read aligns to the graph
changedGraph = insertAlignedRead(self.oneSubstitutionGraph, self.readwithOneDifference)
self.assertFalse(isIsomorphic(self.oneSubstitutionGraph , changedGraph))
self.assertEqual(calculateGED(self.oneSubstitutionGraph, changedGraph), 1.0)
class MultipleSequenceAlignmentTest(unittest.TestCase):
def global_align_test(self):
from gengraph_newfunctions import global_align_by_composition, create_freagment_similarity_table
seq_file = './test_files/s_pneumoniae.txt'
output = create_freagment_similarity_table(seq_file, 100, 50)
self.assertEqual(output, 'dataframe')
def align_one_read(self):
self.assertEqual('this', 'this')
class HashTesting(unittest.TestCase):
def test_one(self):
self.assertEqual('dataframe', 'dataframe')
if __name__ == '__main__':
unittest.main()