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_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_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_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_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 run_pangtree(maf_path: Path, fasta_path: Path, output_dir: Path,
po_output: bool) -> None:
output_dir = pathtools.get_child_dir(output_dir,
pathtools.get_current_time())
print(f"Runing pangtree for maf: {maf_path} and fasta: {fasta_path} "
f"Output in: {output_dir}, include po file: {po_output}.")
fasta_provider = missings.FromFile(fasta_path)
maf = msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path)
poagraph, dagmaf = builder.build_from_dagmaf(maf, fasta_provider)
for p in p_values:
current_output_dir = pathtools.get_child_dir(output_dir,
str(p).replace(".", "_"))
stop = at_params.Stop(0.99)
at = at_builders.build_affinity_tree(poagraph, None,
current_output_dir, stop,
at_params.P(p), True)
at_newick = at.as_newick(None, separate_leaves=True)
pathtools.save_to_file(
at_newick,
pathtools.get_child_path(current_output_dir,
"affinity_tree.newick"))
if po_output:
pangenome_po = po.poagraph_to_PangenomePO(poagraph)
pathtools.save_to_file(
pangenome_po,
pathtools.get_child_path(current_output_dir, "poagraph.po"))
task_params = json.TaskParameters(
multialignment_file_path=str(maf_path),
multialignment_format="maf",
datatype="nucleotides",
blosum_file_path="",
output_path=current_output_dir,
fasta_provider=fasta_provider,
fasta_source_file=fasta_path,
consensus_type="tree",
stop=str(stop),
p=str(p),
output_with_nodes=False)
pangenomejson = json.to_PangenomeJSON(task_parameters=task_params,
poagraph=poagraph,
dagmaf=dagmaf,
affinity_tree=at)
pangenome_json_str = json.to_json(pangenomejson)
pathtools.save_to_file(
pangenome_json_str,
pathtools.get_child_path(current_output_dir, "pangenome.json"))
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_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 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_10_metadata_feed_to_alignment_from_csv(self, test_name, maf_name,
csv_name, po_name,
expected_metadata):
maf_path = self.alignment_files_dir.joinpath(maf_name)
csv_path = self.csv_files_dir.joinpath(csv_name)
po_path = self.alignment_files_dir.joinpath(po_name)
poagraph, _ = builder.build_from_dagmaf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
self.fasta_provider,
msa.MetadataCSV(pathtools.get_file_content_stringio(csv_path),
csv_path))
actual_metadata = {
seq_id: seq.seqmetadata
for seq_id, seq in poagraph.sequences.items()
}
self.assertEqual(expected_metadata, actual_metadata)
poagraph = builder.build_from_maf(
msa.Maf(pathtools.get_file_content_stringio(maf_path), maf_path),
msa.MetadataCSV(pathtools.get_file_content_stringio(csv_path),
csv_path))
actual_metadata = {
seq_id: seq.seqmetadata
for seq_id, seq in poagraph.sequences.items()
}
self.assertEqual(expected_metadata, actual_metadata)
poagraph = builder.build_from_po(
msa.Po(pathtools.get_file_content_stringio(po_path), maf_path),
msa.MetadataCSV(pathtools.get_file_content_stringio(csv_path),
csv_path))
actual_metadata = {
seq_id: seq.seqmetadata
for seq_id, seq in poagraph.sequences.items()
}
self.assertEqual(expected_metadata, actual_metadata)
def run_pangtreebuild(output_dir: Path,
datatype: DataType,
multialignment: Union[Maf, Po],
fasta_provider: Union[FromFile, FromNCBI,
ConstBaseProvider],
blosum: Blosum,
consensus_choice: str,
output_po: bool,
output_fasta: bool,
output_newick: bool,
missing_symbol: MissingBase,
metadata: Optional[MetadataCSV] = None,
hbmin: Optional[Hbmin] = None,
stop: Optional[Stop] = None,
p: Optional[P] = None,
fasta_path: Optional[Path] = None,
include_nodes: Optional[bool] = None) -> PangenomeJSON:
start = time.time()
logprocess.add_file_handler_to_logger(output_dir,
"details",
"details.log",
propagate=False)
logprocess.add_file_handler_to_logger(output_dir,
"",
"details.log",
propagate=False)
logprocess.remove_console_handler_from_root_logger()
poagraph, dagmaf = None, None
if isinstance(multialignment, Maf):
poagraph, dagmaf = builder.build_from_dagmaf(multialignment,
fasta_provider, metadata)
elif isinstance(multialignment, Po):
poagraph = builder.build_from_po(multialignment, metadata)
consensus_output_dir = tools.get_child_dir(output_dir, "consensus")
consensus_tree = None
if consensus_choice == 'poa':
consensus_tree = build_poa_affinity_tree(poagraph, blosum,
consensus_output_dir, hbmin,
True)
elif consensus_choice == 'tree':
consensus_tree = build_affinity_tree(poagraph, blosum,
consensus_output_dir, stop, p,
True)
if output_po:
pangenome_po = poagraph_to_PangenomePO(poagraph)
tools.save_to_file(pangenome_po,
tools.get_child_path(output_dir, "poagraph.po"))
if output_fasta:
sequences_fasta = poagraph_to_fasta(poagraph)
tools.save_to_file(sequences_fasta,
tools.get_child_path(output_dir, "sequences.fasta"))
if consensus_tree:
consensuses_fasta = affinity_tree_to_fasta(poagraph,
consensus_tree)
tools.save_to_file(
consensuses_fasta,
tools.get_child_path(output_dir, "consensuses.fasta"))
if output_newick:
if metadata is not None:
seq_id_to_metadata = {
seq_id: seq.seqmetadata
for seq_id, seq in poagraph.sequences.items()
}
else:
seq_id_to_metadata = None
affinity_tree_newick = consensus_tree.as_newick(seq_id_to_metadata,
separate_leaves=True)
tools.save_to_file(
affinity_tree_newick,
tools.get_child_path(output_dir, "affinity_tree.newick"))
end = time.time()
task_parameters = TaskParameters(
running_time=f"{end - start}s",
multialignment_file_path=multialignment.filename,
multialignment_format=str(type(multialignment).__name__),
datatype=datatype.name,
metadata_file_path=metadata.filename if metadata else None,
blosum_file_path=blosum.filepath.name,
output_path=None,
output_po=output_po,
output_fasta=output_fasta,
output_with_nodes=include_nodes,
verbose=True,
raw_maf=False,
fasta_provider=str(type(fasta_provider).__name__),
missing_base_symbol=missing_symbol.value,
fasta_source_file=fasta_path,
consensus_type=consensus_choice,
hbmin=hbmin.value if hbmin else None,
stop=stop.value if stop else None,
p=p.value if p else None)
pangenomejson = to_PangenomeJSON(task_parameters=task_parameters,
poagraph=poagraph,
dagmaf=dagmaf,
affinity_tree=consensus_tree)
pangenome_json_str = to_json(pangenomejson)
tools.save_to_file(pangenome_json_str,
tools.get_child_path(output_dir, "pangenome.json"))
return pangenomejson
def main():
parser = cli.get_parser()
args = parser.parse_args()
start = datetime.datetime.now()
if not args.quiet and args.verbose:
logprocess.add_file_handler_to_logger(args.output_dir,
"details",
"details.log",
propagate=False)
logprocess.add_file_handler_to_logger(args.output_dir,
"",
"details.log",
propagate=False)
if args.quiet:
logprocess.disable_all_loggers()
poagraph, dagmaf, fasta_provider = None, None, None
if isinstance(args.multialignment, msa.Maf) and args.raw_maf:
poagraph = builder.build_from_maf(args.multialignment, args.metadata)
elif isinstance(args.multialignment, msa.Maf) and not args.raw_maf:
fasta_provider = cli.resolve_fasta_provider(args)
poagraph, dagmaf = builder.build_from_dagmaf(args.multialignment,
fasta_provider,
args.metadata)
elif isinstance(args.multialignment, msa.Po):
poagraph = builder.build_from_po(args.multialignment, args.metadata)
affinity_tree = None
if args.affinity is not None:
blosum = args.blosum if args.blosum else cli.get_default_blosum()
if fasta_provider is not None and isinstance(
fasta_provider, missings.ConstBaseProvider):
blosum.check_if_symbol_is_present(
fasta_provider.missing_base.as_str())
consensus_output_dir = pathtools.get_child_dir(args.output_dir,
"affinitytree")
if args.affinity == 'poa':
affinity_tree = at_builders.build_poa_affinity_tree(
poagraph, blosum, consensus_output_dir, args.hbmin,
args.verbose)
elif args.affinity == 'tree':
affinity_tree = at_builders.build_affinity_tree(
poagraph, blosum, consensus_output_dir, args.stop, args.p,
args.verbose)
if args.metadata is not None:
seq_id_to_metadata = {
seq_id: seq.seqmetadata
for seq_id, seq in poagraph.sequences.items()
}
else:
seq_id_to_metadata = None
affinity_tree_newick = affinity_tree.as_newick(seq_id_to_metadata,
separate_leaves=True)
pathtools.save_to_file(
affinity_tree_newick,
pathtools.get_child_path(consensus_output_dir,
"affinity_tree.newick"))
if args.output_po:
pangenome_po = po.poagraph_to_PangenomePO(poagraph)
pathtools.save_to_file(
pangenome_po,
pathtools.get_child_path(args.output_dir, "poagraph.po"))
if args.output_fasta:
sequences_fasta = fasta.poagraph_to_fasta(poagraph)
pathtools.save_to_file(
sequences_fasta,
pathtools.get_child_path(args.output_dir, "_sequences.fasta"))
if affinity_tree:
consensuses_fasta = fasta.affinity_tree_to_fasta(
poagraph, affinity_tree)
pathtools.save_to_file(
consensuses_fasta,
pathtools.get_child_path(args.output_dir,
"affinitytree.fasta"))
end = datetime.datetime.now()
pangenomejson = json.to_PangenomeJSON(
task_parameters=cli.get_task_parameters(args,
running_time=f"{end-start}s"),
poagraph=poagraph,
dagmaf=dagmaf,
affinity_tree=affinity_tree)
pangenome_json_str = json.to_json(pangenomejson)
pathtools.save_to_file(
pangenome_json_str,
pathtools.get_child_path(args.output_dir, "pangenome.json"))
