def test_3_cycle_f_f_f(self):
graph = nx.Graph()
graph.add_edges_from([('Contig1', 'Contig2'), ('Contig2', 'Contig3'),
('Contig3', 'Contig1')])
contig_ends = {
'Contig1': {
'Contig2': (100, 1),
'Contig3': (1, 100)
},
'Contig2': {
'Contig1': (1, 100),
'Contig3': (100, 1)
},
'Contig3': {
'Contig1': (100, 1),
'Contig2': (1, 100)
}
}
assembly = Assembly('madansi/tests/data/assembly_7_sequences.fa')
assembly.sequence_names()
graph_to_fasta = GraphToFasta(assembly.sequences, graph, 'output.fa',
contig_ends)
self.assertEqual(
graph_to_fasta.walk_contig_graph(['Contig2', 'Contig1',
'Contig3']),
['Contig1', 'Contig2', 'Contig3'])
self.assertDictEqual(graph_to_fasta.contig_orientation, {
'Contig1': 1,
'Contig2': 1,
'Contig3': 1
})
def test_walk_contig_graph(self):
graph = nx.Graph()
graph.add_edges_from([('Contig1', 'Contig2'), ('Contig2', 'Contig3'),
('Contig3', 'Contig4')])
contig_ends = {
'Contig1': {
'Contig2': (1, 100)
},
'Contig2': {
'Contig1': (29, 102),
'Contig3': (307, 240)
},
'Contig3': {
'Contig2': (1000, 891),
'Contig4': (201, 401)
},
'Contig4': {
'Contig3': (49, 300)
}
}
assembly = Assembly('madansi/tests/data/assembly_4_sequences.fa')
assembly.sequence_names()
graph_to_fasta = GraphToFasta(assembly.sequences, graph, 'output.fa',
contig_ends)
self.assertEqual(['Contig1', 'Contig2', 'Contig3', 'Contig4'],
graph_to_fasta.walk_contig_graph(
['Contig1', 'Contig2', 'Contig3', 'Contig4']))
def test_walk_contig_graph_contig_high_degree(self):
contig_ends = { 'Contig1':{'Contig2':(1,100)},\
'Contig2':{'Contig1':(29, 102), 'Contig3':(307, 240)},\
'Contig3':{'Contig2':(1000, 891), 'Contig4':(201, 401)},\
'Contig4':{'Contig3':(49, 300), 'Contig5':(102, 30), 'Contig7':(401,209)},\
'Contig5':{'Contig4':(1,302), 'Contig6':(1,100)},\
'Contig6':{'Contig5':(8,912)},\
'Contig7':{'Contig4':(1,20)}}
graph = nx.Graph()
graph.add_edges_from([('Contig1', 'Contig2'), ('Contig2', 'Contig3'),
('Contig4', 'Contig5')])
assembly = Assembly('madansi/tests/data/assembly_7_sequences.fa')
assembly.sequence_names()
graph_to_fasta = GraphToFasta(assembly.sequences, graph, 'output.fa',
contig_ends)
self.assertEqual(
graph_to_fasta.walk_contig_graph(['Contig1', 'Contig2',
'Contig3']),
['Contig1', 'Contig2', 'Contig3'])
graph_to_fasta.create_fasta_file_combined_contigs()
self.assertTrue(
filecmp.cmp('madansi/tests/data/combine_contigs.fa', 'output.fa'))
os.unlink('output.fa')