def test_04_single_block_no_nucleotides(self):
maf_path = self.maf_files_dir.joinpath(
"test_4_single_block_no_nucleotides.maf")
expected_nodes = []
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[],
graph.SequenceMetadata({'group': '2'}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider,
self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
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_05_single_block_single_nucletodide(self):
maf_path = self.maf_files_dir.joinpath(
"test_5_single_block_single_nucletodide.maf")
expected_nodes = [
graph.Node(node_id=nid(0), base=graph.Base('A'), aligned_to=None, block_id=bid(0))
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [0])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [0])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [0])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[graph.SeqPath([*map(nid, [0])])],
graph.SequenceMetadata({'group': '2'}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider,
self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
def test_7_missing_one_reverted_sequence_middle_minus1_minus1(self):
maf_path = self.maf_files_dir.joinpath(
"test_7_missing_one_reverted_sequence_middle_minus1_minus1.maf")
expected_nodes = [
# block 0
graph.Node(node_id=nid(0), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(1), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(2), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(3), base=graph.Base('A'), aligned_to=None),
# missing seq2
graph.Node(node_id=nid(4),
base=graph.Base(self.missing_n.value),
aligned_to=None),
graph.Node(node_id=nid(5),
base=graph.Base(self.missing_n.value),
aligned_to=None),
# block 1
graph.Node(node_id=nid(6), base=graph.Base('A'),
aligned_to=nid(7)),
graph.Node(node_id=nid(7), base=graph.Base('G'),
aligned_to=nid(6)),
graph.Node(node_id=nid(8), base=graph.Base('C'),
aligned_to=nid(9)),
graph.Node(node_id=nid(9), base=graph.Base('G'),
aligned_to=nid(8)),
graph.Node(node_id=nid(10),
base=graph.Base('C'),
aligned_to=nid(11)),
graph.Node(node_id=nid(11),
base=graph.Base('T'),
aligned_to=nid(10)),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'), [],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(
msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [0, 1, 2, 3, 7, 9, 11])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(
msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [0, 1, 4, 5, 6, 8, 10])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'), [],
graph.SequenceMetadata({'group': '2'}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
missings.ConstBaseProvider(self.missing_n), self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
def test_09_inactive_edges_but_all_strands_plus(self):
maf_path = self.maf_files_dir.joinpath("test_9_inactive_edges_but_all_strands_plus.maf")
expected_nodes = [
graph.Node(node_id=nid(0), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(1), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(2), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(3), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(4), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(5), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(6), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(7), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(8), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(9), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(10), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(11), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(12), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(13), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(14), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(15), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(16), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(17), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(18), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(19), base=graph.Base('G'), aligned_to=None),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [0, 1, 2, 3, 4, 10, 11, 12, 13, 14])]),
graph.SeqPath([*map(nid, [5, 6, 7, 8, 9, 15, 16, 17, 18, 19])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[],
graph.SequenceMetadata({'group': '2'})),
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider,
self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
def test_10_parallel_blocks_1st_and_2nd_merge_into_3rd(self):
maf_path = self.maf_files_dir.joinpath("test_10_parallel_blocks_1st_and_2nd_merge_into_3rd.maf")
expected_nodes = [
graph.Node(node_id=nid(0), base=graph.Base('G'), aligned_to=nid(1)),
graph.Node(node_id=nid(1), base=graph.Base('T'), aligned_to=nid(0)),
graph.Node(node_id=nid(2), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(3), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(4), base=graph.Base('C'), aligned_to=nid(5)),
graph.Node(node_id=nid(5), base=graph.Base('G'), aligned_to=nid(4)),
graph.Node(node_id=nid(6), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(7), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(8), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(9), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(10), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(11), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(12), base=graph.Base('C'), aligned_to=nid(13)),
graph.Node(node_id=nid(13), base=graph.Base('G'), aligned_to=nid(12)),
graph.Node(node_id=nid(14), base=graph.Base('C'), aligned_to=nid(15)),
graph.Node(node_id=nid(15), base=graph.Base('G'), aligned_to=nid(16)),
graph.Node(node_id=nid(16), base=graph.Base('T'), aligned_to=nid(14)),
graph.Node(node_id=nid(17), base=graph.Base('A'), aligned_to=nid(18)),
graph.Node(node_id=nid(18), base=graph.Base('T'), aligned_to=nid(17)),
graph.Node(node_id=nid(19), base=graph.Base('A'), aligned_to=nid(20)),
graph.Node(node_id=nid(20), base=graph.Base('C'), aligned_to=nid(19)),
graph.Node(node_id=nid(21), base=graph.Base('C'), aligned_to=nid(22)),
graph.Node(node_id=nid(22), base=graph.Base('G'), aligned_to=nid(21)),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [7, 8, 9, 10, 11, 12, 15, 18, 19, 21])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [7, 8, 9, 10, 11, 12, 15, 18, 19, 21])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [0, 2, 3, 4, 6, 13, 16, 17, 20, 21])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[graph.SeqPath([*map(nid, [1, 2, 3, 5, 6, 13, 14, 17, 20, 22])])],
graph.SequenceMetadata({'group': '2'})),
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider,
self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
def test_6_missing_one_reverted_sequence_middle_minus1_1(self):
maf_path = self.maf_files_dir.joinpath(
"test_6_missing_one_reverted_sequence_middle_minus1_1.maf")
expected_nodes = [
# block 1 because it is first in DAG and reverted
graph.Node(node_id=nid(0), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(1), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(2), base=graph.Base('C'),
aligned_to=nid(3)),
graph.Node(node_id=nid(3), base=graph.Base('T'),
aligned_to=nid(2)),
# missing seq2, on edge (-1,1)
graph.Node(node_id=nid(4), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(5), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(6), base=graph.Base('A'),
aligned_to=nid(7)),
graph.Node(node_id=nid(7), base=graph.Base('C'),
aligned_to=nid(6)),
graph.Node(node_id=nid(8), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(9), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(10),
base=graph.Base('A'),
aligned_to=nid(11)),
graph.Node(node_id=nid(11),
base=graph.Base('C'),
aligned_to=nid(10)),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'), [],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'), [
graph.SeqPath([*map(nid, [0, 1, 2])]),
graph.SeqPath([*map(nid, [6, 8, 9, 10])])
], graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(
msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [0, 1, 3, 4, 5, 7, 11])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'), [],
graph.SequenceMetadata({'group': '2'}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider, self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
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_1_p_parameter_influence(self, p: at_params.P,
expected_cutoff: graph.Compatibility):
nodes = [
graph.Node(node_id=nid(0), base=b('T'), aligned_to=None),
graph.Node(node_id=nid(1), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(2), base=b('G'), aligned_to=None),
graph.Node(node_id=nid(3), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(4), base=b('C'), aligned_to=None),
graph.Node(node_id=nid(5), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(6), base=b('C'), aligned_to=None),
graph.Node(node_id=nid(7), base=b('G'), aligned_to=None),
graph.Node(node_id=nid(8), base=b('T'), aligned_to=None),
graph.Node(node_id=nid(9), base=b('A'), aligned_to=None)
]
sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'), [
graph.SeqPath(
[*map(nid, [10, 11, 12, 13, 14, 15, 16, 17, 18, 9])])
], graph.SequenceMetadata({})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'), [
graph.SeqPath(
[*map(nid, [10, 11, 12, 13, 14, 15, 16, 17, 8, 9])])
], graph.SequenceMetadata({})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'), [
graph.SeqPath(
[*map(nid, [10, 11, 12, 13, 14, 15, 16, 7, 8, 9])])
], graph.SequenceMetadata({})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'), [
graph.SeqPath([*map(nid, [10, 11, 12, 3, 4, 5, 6, 7, 8, 9])])
], graph.SequenceMetadata({})),
msa.SequenceID('seq4'):
graph.Sequence(
msa.SequenceID('seq3'),
[graph.SeqPath([*map(nid, [10, 11, 2, 3, 4, 5, 6, 7, 8, 9])])],
graph.SequenceMetadata({}))
}
poagraph = graph.Poagraph(nodes, sequences)
consensus_path = graph.SeqPath(
[*map(nid, [10, 11, 12, 13, 14, 15, 16, 17, 18, 19])])
compatibilities = poagraph.get_compatibilities(
poagraph.get_sequences_ids(), consensus_path, p)
actual_cutoff = at_builders._find_node_cutoff(
[c for c in compatibilities.values()], []).cutoff
self.assertAlmostEqual(expected_cutoff.value, actual_cutoff.value)
def test_1_typical_poagraph(self):
po_path = self.po_files_dir.joinpath("test_1.po")
expected_nodes = [
graph.Node(node_id=nid(0), base=bid('A'), aligned_to=nid(1)),
graph.Node(node_id=nid(1), base=bid('G'), aligned_to=nid(0)),
graph.Node(node_id=nid(2), base=bid('C'), aligned_to=nid(3)),
graph.Node(node_id=nid(3), base=bid('G'), aligned_to=nid(2)),
graph.Node(node_id=nid(4), base=bid('A'), aligned_to=nid(5)),
graph.Node(node_id=nid(5), base=bid('T'), aligned_to=nid(4)),
graph.Node(node_id=nid(6), base=bid('G'), aligned_to=None),
graph.Node(node_id=nid(7), base=bid('G'), aligned_to=None),
graph.Node(node_id=nid(8), base=bid('A'), aligned_to=nid(9)),
graph.Node(node_id=nid(9), base=bid('C'), aligned_to=nid(10)),
graph.Node(node_id=nid(10), base=bid('G'), aligned_to=nid(11)),
graph.Node(node_id=nid(11), base=bid('T'), aligned_to=nid(8)),
graph.Node(node_id=nid(12), base=bid('A'), aligned_to=nid(13)),
graph.Node(node_id=nid(13), base=bid('C'), aligned_to=nid(12)),
graph.Node(node_id=nid(14), base=bid('T'), aligned_to=None),
graph.Node(node_id=nid(15), base=bid('A'), aligned_to=nid(16)),
graph.Node(node_id=nid(16), base=bid('C'), aligned_to=nid(17)),
graph.Node(node_id=nid(17), base=bid('G'), aligned_to=nid(15))
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(
msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [0, 2, 4, 6, 7, 8, 12, 14, 16])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [1, 2, 5, 6, 7, 9])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(
msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [3, 4, 6, 7, 10, 12, 14, 17])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[graph.SeqPath([*map(nid, [11, 13, 14, 15])])],
graph.SequenceMetadata({'group': '2'}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
nodes, sequences = po2poagraph.get_poagraph(
msa.Po(pathtools.get_file_content_stringio(po_path), po_path),
self.metadatacsv)
actual_poagraph = graph.Poagraph(nodes, sequences)
self.assertEqual(expected_poagraph, actual_poagraph)
def test_2_missing_sequence_end(self):
maf_path = self.maf_files_dir.joinpath(
"test_2_missing_sequence_end.maf")
expected_nodes = [
graph.Node(node_id=nid(0), base=graph.Base('A'),
aligned_to=nid(1)),
graph.Node(node_id=nid(1), base=graph.Base('G'),
aligned_to=nid(0)),
graph.Node(node_id=nid(2), base=graph.Base('C'),
aligned_to=nid(3)),
graph.Node(node_id=nid(3), base=graph.Base('G'),
aligned_to=nid(2)),
graph.Node(node_id=nid(4), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(5), base=graph.Base('A'),
aligned_to=nid(6)),
graph.Node(node_id=nid(6), base=graph.Base('C'),
aligned_to=nid(5)),
graph.Node(node_id=nid(7), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(8), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(9), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(10), base=graph.Base('T'), aligned_to=None),
graph.Node(node_id=nid(11), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(12), base=graph.Base('T'), aligned_to=None),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'), [],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(
msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [0, 2, 4, 5, 8, 9, 10])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(
msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [1, 3, 4, 6, 7, 11, 12])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'), [],
graph.SequenceMetadata({'group': '2'}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider, self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
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_1_typical_poagraph(self):
expected_po_content_path = self.po_files_dir.joinpath("test_1.po")
poagraph_nodes = [graph.Node(node_id=nid(0), base=bid('A'), aligned_to=nid(1)),
graph.Node(node_id=nid(1), base=bid('G'), aligned_to=nid(0)),
graph.Node(node_id=nid(2), base=bid('C'), aligned_to=nid(3)),
graph.Node(node_id=nid(3), base=bid('G'), aligned_to=nid(2)),
graph.Node(node_id=nid(4), base=bid('A'), aligned_to=nid(5)),
graph.Node(node_id=nid(5), base=bid('T'), aligned_to=nid(4)),
graph.Node(node_id=nid(6), base=bid('G'), aligned_to=None),
graph.Node(node_id=nid(7), base=bid('G'), aligned_to=None),
graph.Node(node_id=nid(8), base=bid('A'), aligned_to=nid(9)),
graph.Node(node_id=nid(9), base=bid('C'), aligned_to=nid(10)),
graph.Node(node_id=nid(10), base=bid('G'), aligned_to=nid(11)),
graph.Node(node_id=nid(11), base=bid('T'), aligned_to=nid(8)),
graph.Node(node_id=nid(12), base=bid('A'), aligned_to=nid(13)),
graph.Node(node_id=nid(13), base=bid('C'), aligned_to=nid(12)),
graph.Node(node_id=nid(14), base=bid('T'), aligned_to=None),
graph.Node(node_id=nid(15), base=bid('A'), aligned_to=nid(16)),
graph.Node(node_id=nid(16), base=bid('C'), aligned_to=nid(17)),
graph.Node(node_id=nid(17), base=bid('G'), aligned_to=nid(15))
]
poagraph_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [0, 2, 4, 6, 7, 8, 12, 14, 16])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [1, 2, 5, 6, 7, 9])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [3, 4, 6, 7, 10, 12, 14, 17])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[graph.SeqPath([*map(nid, [11, 13, 14, 15])])],
graph.SequenceMetadata({'group': '1'})),
}
poagraph = graph.Poagraph(poagraph_nodes, poagraph_sequences)
actual_po_content = po.poagraph_to_PangenomePO(poagraph)
expected_po_content = pathtools.get_file_content(expected_po_content_path)
self.assertEqual(expected_po_content, actual_po_content)
def test_2_consensuses_and_empty_sequences(self):
expected_po_content_path = self.po_files_dir.joinpath("test_2.po")
poagraph_nodes = [graph.Node(node_id=nid(0), base=bid('C'), aligned_to=nid(1)),
graph.Node(node_id=nid(1), base=bid('T'), aligned_to=nid(0)),
graph.Node(node_id=nid(2), base=bid('A'), aligned_to=nid(3)),
graph.Node(node_id=nid(3), base=bid('G'), aligned_to=nid(2)),
graph.Node(node_id=nid(4), base=bid('C'), aligned_to=None),
graph.Node(node_id=nid(5), base=bid('T'), aligned_to=None),
graph.Node(node_id=nid(6), base=bid('A'), aligned_to=nid(7)),
graph.Node(node_id=nid(7), base=bid('T'), aligned_to=nid(6)),
graph.Node(node_id=nid(8), base=bid('G'), aligned_to=None)
]
poagraph_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [0, 3, 4, 5, 6, 8])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [1, 2, 4, 5, 7, 8])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('CONSENS0'):
graph.Sequence(msa.SequenceID('CONSENS0'),
[graph.SeqPath([*map(nid, [0, 3, 4, 5, 7, 8])])],
None),
msa.SequenceID('CONSENS1'):
graph.Sequence(msa.SequenceID('CONSENS1'),
[graph.SeqPath([*map(nid, [1, 2, 4, 5, 6, 8])])],
None),
}
poagraph = graph.Poagraph(poagraph_nodes, poagraph_sequences)
actual_po_content = po.poagraph_to_PangenomePO(poagraph)
expected_po_content = pathtools.get_file_content(expected_po_content_path)
self.assertEqual(expected_po_content, actual_po_content)
def test_06_1st_block_separates_into_2_branches_which_connect_in_3rd_block(self):
maf_path = self.maf_files_dir.joinpath(
"test_6_1st_block_separates_into_2_branches_which_connect_in_3rd_block.maf")
expected_nodes = [
graph.Node(node_id=nid(0), base=graph.Base('A'), aligned_to=nid(1)),
graph.Node(node_id=nid(1), base=graph.Base('C'), aligned_to=nid(2)),
graph.Node(node_id=nid(2), base=graph.Base('G'), aligned_to=nid(0)),
graph.Node(node_id=nid(3), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(4), base=graph.Base('A'), aligned_to=nid(5)),
graph.Node(node_id=nid(5), base=graph.Base('T'), aligned_to=nid(4)),
graph.Node(node_id=nid(6), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(7), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(8), base=graph.Base('C'), aligned_to=nid(9)),
graph.Node(node_id=nid(9), base=graph.Base('G'), aligned_to=nid(10)),
graph.Node(node_id=nid(10), base=graph.Base('T'), aligned_to=nid(8)),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [0, 3, 4, 8])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [1, 3, 5, 6, 7, 9])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [2, 3, 5, 10])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[],
graph.SequenceMetadata({'group': '2'}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider,
self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
def setUp(self):
nodes = [
graph.Node(
node_id=nid(0),
base=b('T'),
aligned_to=None,
),
graph.Node(node_id=nid(1), base=b('A'), aligned_to=nid(2)),
graph.Node(node_id=nid(2), base=b('G'), aligned_to=nid(1)),
graph.Node(node_id=nid(3), base=b('A'), aligned_to=nid(4)),
graph.Node(node_id=nid(4), base=b('C'), aligned_to=nid(3)),
graph.Node(node_id=nid(5), base=b('A'), aligned_to=nid(6)),
graph.Node(node_id=nid(6), base=b('C'), aligned_to=nid(7)),
graph.Node(node_id=nid(7), base=b('G'), aligned_to=nid(8)),
graph.Node(node_id=nid(8), base=b('T'), aligned_to=nid(5)),
graph.Node(node_id=nid(9), base=b('A'), aligned_to=None),
graph.Node(node_id=nid(10), base=b('C'), aligned_to=nid(11)),
graph.Node(node_id=nid(11), base=b('T'), aligned_to=nid(10)),
graph.Node(node_id=nid(12), base=b('G'), aligned_to=None),
graph.Node(node_id=nid(13), base=b('A'), aligned_to=nid(14)),
graph.Node(node_id=nid(14), base=b('C'), aligned_to=nid(13))
]
sequences = {
msa.SequenceID('seq0'):
graph.Sequence(
msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [0, 1, 3, 5, 9, 10, 13])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [1, 3, 6, 9, 11])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [2, 4, 7, 9, 11, 12])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq3'):
graph.Sequence(
msa.SequenceID('seq3'),
[graph.SeqPath([*map(nid, [2, 4, 8, 9, 11, 12, 14])])],
graph.SequenceMetadata({'group': '1'})),
}
self.poagraph = graph.Poagraph(nodes, sequences)
def test_02_seq_starts_in_second_block(self):
maf_path = self.maf_files_dir.joinpath(
"test_2_seq_starts_in_second_block.maf")
expected_nodes = [
graph.Node(node_id=nid(0), base=graph.Base('C'), aligned_to=None, block_id=bid(0)),
graph.Node(node_id=nid(1), base=graph.Base('T'), aligned_to=None, block_id=bid(0)),
graph.Node(node_id=nid(2), base=graph.Base('G'), aligned_to=None, block_id=bid(0)),
graph.Node(node_id=nid(3), base=graph.Base('T'), aligned_to=None, block_id=bid(1)),
graph.Node(node_id=nid(4), base=graph.Base('G'), aligned_to=nid(5), block_id=bid(2)),
graph.Node(node_id=nid(5), base=graph.Base('T'), aligned_to=nid(4), block_id=bid(2)),
graph.Node(node_id=nid(6), base=graph.Base('A'), aligned_to=None, block_id=bid(2)),
graph.Node(node_id=nid(7), base=graph.Base('A'), aligned_to=None, block_id=bid(2)),
graph.Node(node_id=nid(8), base=graph.Base('C'), aligned_to=None, block_id=bid(2)),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [1, 2, 3])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [0, 5, 7])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [3, 4, 6, 8])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[],
graph.SequenceMetadata({'group': '2'}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider,
self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
def test_08_reversed_block(self):
maf_path = self.maf_files_dir.joinpath("test_8_reversed_block.maf")
expected_nodes = [
graph.Node(node_id=nid(0), base=graph.Base('C'), aligned_to=None),
graph.Node(node_id=nid(1), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(2), base=graph.Base('T'), aligned_to=None),
# next block is reversed because it was converted to dag
graph.Node(node_id=nid(3), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(4), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(5), base=graph.Base('A'), aligned_to=nid(6)),
graph.Node(node_id=nid(6), base=graph.Base('G'), aligned_to=nid(5)),
graph.Node(node_id=nid(7), base=graph.Base('A'), aligned_to=None),
graph.Node(node_id=nid(8), base=graph.Base('G'), aligned_to=None),
graph.Node(node_id=nid(9), base=graph.Base('T'), aligned_to=None),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [0, 1, 3, 4, 5, 7, 8, 9])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [0, 1, 2, 3, 4, 6, 7, 8, 9])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'),
[graph.SeqPath([*map(nid, [0, 1, 2, 3, 4, 6, 7, 9])])],
graph.SequenceMetadata({'group': '2'})),
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
actual_poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider,
self.metadatacsv)
self.assertEqual(expected_poagraph, actual_poagraph)
def test_2_consensuses_and_empty_sequences(self):
po_path = self.po_files_dir.joinpath("test_2.po")
expected_nodes = [
graph.Node(node_id=nid(0), base=bid('C'), aligned_to=nid(1)),
graph.Node(node_id=nid(1), base=bid('T'), aligned_to=nid(0)),
graph.Node(node_id=nid(2), base=bid('A'), aligned_to=nid(3)),
graph.Node(node_id=nid(3), base=bid('G'), aligned_to=nid(2)),
graph.Node(node_id=nid(4), base=bid('C'), aligned_to=None),
graph.Node(node_id=nid(5), base=bid('T'), aligned_to=None),
graph.Node(node_id=nid(6), base=bid('A'), aligned_to=nid(7)),
graph.Node(node_id=nid(7), base=bid('T'), aligned_to=nid(6)),
graph.Node(node_id=nid(8), base=bid('G'), aligned_to=None)
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [0, 3, 4, 5, 6, 8])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [1, 2, 4, 5, 7, 8])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(msa.SequenceID('seq2'), [],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'), [],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('CONSENS0'):
graph.Sequence(msa.SequenceID('CONSENS0'),
[graph.SeqPath([*map(nid, [0, 3, 4, 5, 7, 8])])],
graph.SequenceMetadata({})),
msa.SequenceID('CONSENS1'):
graph.Sequence(msa.SequenceID('CONSENS1'),
[graph.SeqPath([*map(nid, [1, 2, 4, 5, 6, 8])])],
graph.SequenceMetadata({}))
}
expected_poagraph = graph.Poagraph(expected_nodes, expected_sequences)
nodes, sequences = po2poagraph.get_poagraph(
msa.Po(pathtools.get_file_content_stringio(po_path), po_path),
self.metadatacsv)
actual_poagraph = graph.Poagraph(nodes, sequences)
self.assertEqual(expected_poagraph, actual_poagraph)
def sm(x):
return graph.SequenceMetadata(x)
def test_1_messy_sequences(self):
maf_path = self.maf_files_dir.joinpath("test_1_messy_sequences.maf")
expected_nodes = [
graph.Node(node_id=nid(0),
base=graph.Base('A'),
aligned_to=None,
block_id=bid(0)),
graph.Node(node_id=nid(1),
base=graph.Base('A'),
aligned_to=nid(2),
block_id=bid(0)),
graph.Node(node_id=nid(2),
base=graph.Base('C'),
aligned_to=nid(1),
block_id=bid(0)),
graph.Node(node_id=nid(3),
base=graph.Base('T'),
aligned_to=None,
block_id=bid(0)),
graph.Node(node_id=nid(4),
base=graph.Base('C'),
aligned_to=nid(5),
block_id=bid(0)),
graph.Node(node_id=nid(5),
base=graph.Base('G'),
aligned_to=nid(4),
block_id=bid(0)),
graph.Node(node_id=nid(6),
base=graph.Base('A'),
aligned_to=None,
block_id=bid(1)),
graph.Node(node_id=nid(7),
base=graph.Base('C'),
aligned_to=None,
block_id=bid(1)),
graph.Node(node_id=nid(8),
base=graph.Base('G'),
aligned_to=None,
block_id=bid(1)),
graph.Node(node_id=nid(9),
base=graph.Base('C'),
aligned_to=nid(10),
block_id=bid(2)),
graph.Node(node_id=nid(10),
base=graph.Base('G'),
aligned_to=nid(9),
block_id=bid(2)),
graph.Node(node_id=nid(11),
base=graph.Base('T'),
aligned_to=None,
block_id=bid(2)),
graph.Node(node_id=nid(12),
base=graph.Base('C'),
aligned_to=None,
block_id=bid(2)),
graph.Node(node_id=nid(13),
base=graph.Base('C'),
aligned_to=None,
block_id=bid(2)),
graph.Node(node_id=nid(14),
base=graph.Base('A'),
aligned_to=None,
block_id=bid(2)),
]
expected_sequences = {
msa.SequenceID('seq0'):
graph.Sequence(
msa.SequenceID('seq0'),
[graph.SeqPath([*map(nid, [1, 3, 4, 6, 8, 9, 11, 12])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq1'):
graph.Sequence(
msa.SequenceID('seq1'),
[graph.SeqPath([*map(nid, [2, 3, 4, 10, 11, 12, 13, 14])])],
graph.SequenceMetadata({'group': '1'})),
msa.SequenceID('seq2'):
graph.Sequence(
msa.SequenceID('seq2'),
[graph.SeqPath([*map(nid, [0, 2, 5, 6, 7, 10, 11, 12, 14])])],
graph.SequenceMetadata({'group': '2'})),
msa.SequenceID('seq3'):
graph.Sequence(msa.SequenceID('seq3'), [],
graph.SequenceMetadata({'group': '2'}))
}
actual_nodes, actual_sequences = maf2poagraph.get_poagraph(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.metadatacsv)
self.assertEqual(expected_nodes, actual_nodes)
self.assertEqual(expected_sequences, actual_sequences)
