def test_subpoagraph_should_omit_edges_2(self):
nodes = [
graph.Node(node_id=nid(0), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(1), base=b('C'), aligned_to=None),
graph.Node(node_id=nid(2), base=b('C'), aligned_to=None)
]
sequences = {
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [0, 2])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [0, 1, 2])])],
graph.SequenceMetadata({'group': '1'}))
}
poagraph = graph.Poagraph(nodes, sequences)
translator = poa._PoagraphPOTranslator(poagraph,
[msa.SequenceID('seq1')])
actual_po_content = translator.get_input_po_content()
expected_po_content = "VERSION=pangenome\n" \
"NAME=pangenome\n" \
"TITLE=pangenome\n" \
"LENGTH=2\n" \
"SOURCECOUNT=1\n" \
"SOURCENAME=seq1\n" \
"SOURCEINFO=2 0 100 -1 seq1\n" \
"a:S0\n" \
"c:L0S0"
self.assertEqual(expected_po_content, actual_po_content)
def test_subpoagraph_construction_full_graph(self):
nodes = [
graph.Node(node_id=nid(0), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(1), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(2), base=b('C'), aligned_to=None),
graph.Node(node_id=nid(3), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(4), base=b('T'), aligned_to=None)
]
sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [0, 1, 2, 3, 4])])],
graph.SequenceMetadata({'group': '1'}))
}
poagraph = graph.Poagraph(nodes, sequences)
translator = poa._PoagraphPOTranslator(poagraph,
[msa.SequenceID('seq0')])
actual_po_content = translator.get_input_po_content()
expected_po_content = "VERSION=pangenome\n" \
"NAME=pangenome\n" \
"TITLE=pangenome\n" \
"LENGTH=5\n" \
"SOURCECOUNT=1\n" \
"SOURCENAME=seq0\n" \
"SOURCEINFO=5 0 100 -1 seq0\n" \
"a:S0\n" \
"a:L0S0\n" \
"c:L1S0\n" \
"a:L2S0\n" \
"t:L3S0"
self.assertEqual(expected_po_content, actual_po_content)
def test_subpoagraph_unfilled_nodes(self):
symbol_for_uknown = '?'
nodes = [
graph.Node(node_id=nid(0), base=b('A'), aligned_to=nid(1)),
graph.Node(node_id=nid(1), base=b('C'), aligned_to=nid(0)),
graph.Node(node_id=nid(2), base=b('G'), aligned_to=None),
graph.Node(node_id=nid(3),
base=b(symbol_for_uknown),
aligned_to=None),
graph.Node(node_id=nid(4),
base=b(symbol_for_uknown),
aligned_to=None),
graph.Node(node_id=nid(5), base=b('G'), aligned_to=None),
graph.Node(node_id=nid(6), base=b('C'), aligned_to=None),
graph.Node(node_id=nid(7), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(5), base=b('T'), aligned_to=None)
]
sequences = {
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [0, 2, 3, 4, 7, 8])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [1, 2, 5, 6, 7, 8])])],
graph.SequenceMetadata({'group': '1'}))
}
poagraph = graph.Poagraph(nodes, sequences)
translator = poa._PoagraphPOTranslator(
poagraph, [msa.SequenceID('seq1'),
msa.SequenceID('seq2')])
actual_po_content = translator.get_input_po_content()
expected_po_content = "VERSION=pangenome\n" \
"NAME=pangenome\n" \
"TITLE=pangenome\n" \
"LENGTH=9\n" \
"SOURCECOUNT=2\n" \
"SOURCENAME=seq1\n" \
"SOURCEINFO=6 0 100 -1 seq1\n" \
"SOURCENAME=seq2\n" \
"SOURCEINFO=6 1 100 -1 seq2\n" \
"a:S0A1\n" \
"c:S1A0\n" \
"g:L0L1S0S1\n" \
f"{symbol_for_uknown}:L2S0\n" \
f"{symbol_for_uknown}:L3S0\n" \
"g:L2S1\n" \
"c:L5S1\n" \
"a:L4L6S0S1\n" \
"t:L7S0S1"
self.assertEqual(expected_po_content, actual_po_content)
def test_read_consensus_path_seq1_only_in_input(self):
translator = poa._PoagraphPOTranslator(self.poagraph,
[msa.SequenceID('seq1')])
_ = translator.get_input_po_content()
poa_lines = [
"VERSION=pangenome\n", "NAME=pangenome\n", "TITLE=pangenome\n",
"LENGTH=5\n", "SOURCECOUNT=2\n", "SOURCENAME=seq1\n",
"SOURCEINFO=5 0 100 0 seq1\n", "SOURCENAME=CONSENS0\n",
"SOURCEINFO=5 0 100 0 CONSENS0\n", "a:S0S1\n", "a:L0S0S1\n",
"c:L1S0S1\n", "a:L2S0S1\n", "t:L2S0S1"
]
actual_consensus_path = translator.read_consensus_paths(poa_lines, [0])
expected_consensus_path = [1, 3, 6, 9, 11]
self.assertEqual(expected_consensus_path,
actual_consensus_path[0].path)
def test_subpoagraph_construction_from_poagraph_keep_seq3(self):
translator = poa._PoagraphPOTranslator(self.poagraph,
[msa.SequenceID('seq3')])
actual_po_content = translator.get_input_po_content()
expected_po_content = "VERSION=pangenome\n" \
"NAME=pangenome\n" \
"TITLE=pangenome\n" \
"LENGTH=7\n" \
"SOURCECOUNT=1\n" \
"SOURCENAME=seq3\n" \
"SOURCEINFO=7 0 100 -1 seq3\n" \
"g:S0\n" \
"c:L0S0\n" \
"t:L1S0\n" \
"a:L2S0\n" \
"t:L3S0\n" \
"g:L4S0\n" \
"c:L5S0"
self.assertEqual(expected_po_content, actual_po_content)
def test_subpoagraph_construction_from_poagraph_keep_seq_0_1(self):
translator = poa._PoagraphPOTranslator(
self.poagraph, [msa.SequenceID('seq0'),
msa.SequenceID('seq1')])
actual_po_content = translator.get_input_po_content()
expected_po_content = "VERSION=pangenome\n"\
"NAME=pangenome\n"\
"TITLE=pangenome\n"\
"LENGTH=9\n"\
"SOURCECOUNT=2\n"\
"SOURCENAME=seq0\n"\
"SOURCEINFO=7 0 0 -1 seq0\n"\
"SOURCENAME=seq1\n"\
"SOURCEINFO=5 1 100 -1 seq1\n"\
"t:S0\n"\
"a:L0S0S1\n"\
"a:L1S0S1\n"\
"a:L2S0A4\n"\
"c:L2S1A3\n"\
"a:L3L4S0S1\n"\
"c:L5S0A7\n"\
"t:L5S1A6\n"\
"a:L6S0"
self.assertEqual(expected_po_content, actual_po_content)