def get_ebola_consensus_tree(p: float, stop: float, output_dir_name: str) -> Tuple[Poagraph, AffinityTree]:
current_path = Path(os.path.abspath(__file__)).resolve()
output_dir_path = pathtools.get_child_dir(current_path.parent, output_dir_name)
consensus_output_dir = pathtools.get_child_dir(output_dir_path, "consensus")
multialignment_path = current_path.parent.joinpath("../data/Ebola/genome_whole/input/multialignment.maf")
metadata_path = current_path.parent.joinpath("../data/Ebola/genome_whole/input/metadata.csv")
blosum_path = current_path.parent.joinpath("../bin/blosum80.mat")
fasta_provider = fp_ncbi.FromNCBI(use_cache=True)
multialignment_content = pathtools.get_file_content_stringio(multialignment_path)
multialignment = Maf(file_content=multialignment_content, filename=multialignment_path)
metadata_content = pathtools.get_file_content_stringio(metadata_path)
metadata = MetadataCSV(filecontent=metadata_content, filename=metadata_path)
poagraph, dagmaf = Poagraph.build_from_dagmaf(multialignment, fasta_provider, metadata)
blosum_content = pathtools.get_file_content_stringio(path=blosum_path)
blosum = Blosum(blosum_content, blosum_path)
return poagraph, atree_builders.get_affinity_tree(poagraph,
blosum,
consensus_output_dir,
Stop(stop),
P(p),
False)
def get_ebola_affinity_tree(
p: float, stop: float,
output_dir_name: str) -> Tuple[Poagraph, AffinityTree]:
current_path = Path(os.path.abspath(__file__)).resolve()
output_dir_path = pathtools.get_child_dir(current_path.parent,
output_dir_name)
consensus_output_dir = pathtools.get_child_dir(output_dir_path,
"consensus")
multialignment_path = current_path.parent.joinpath(
"../data/Ebola/multialignment.maf")
metadata_path = current_path.parent.joinpath("../data/Ebola/metadata.csv")
blosum_path = current_path.parent.joinpath("../bin/blosum80.mat")
tp = TaskParameters(running_time="",
multialignment_file_path=multialignment_path,
multialignment_format="MAF",
datatype="N",
metadata_file_path=metadata_path,
blosum_file_path=blosum_path,
output_path=output_dir_path,
output_po=False,
output_fasta=False,
output_with_nodes=False,
verbose=False,
raw_maf=False,
fasta_provider='FromNCBI',
cache=True,
missing_base_symbol="",
fasta_source_file=None,
consensus_type="",
hbmin=0.8,
stop=stop,
p=p)
fasta_provider = fp_ncbi.FromNCBI(use_cache=True)
multialignment_content = pathtools.get_file_content_stringio(
multialignment_path)
multialignment = Maf(file_content=multialignment_content,
filename=multialignment_path)
metadata_content = pathtools.get_file_content_stringio(metadata_path)
metadata = MetadataCSV(filecontent=metadata_content,
filename=metadata_path)
poagraph, dagmaf = Poagraph.build_from_dagmaf(multialignment,
fasta_provider, metadata)
blosum_content = pathtools.get_file_content_stringio(path=blosum_path)
blosum = Blosum(blosum_content, blosum_path)
return poagraph, atree_builders.get_affinity_tree(poagraph, blosum,
consensus_output_dir,
Stop(stop), P(p), False)
def get_ebola_consensus_tree(p: float, stop: float, output_dir_name: str) -> Tuple[Poagraph, ConsensusTree]:
current_path = Path(os.path.abspath(__file__)).resolve()
output_dir_path = pathtools.get_child_dir(current_path.parent, output_dir_name)
consensus_output_dir = pathtools.get_child_dir(output_dir_path, "consensus")
multialignment_path = current_path.parent.joinpath("../data/Ebola/genome_whole/input/multialignment.maf")
metadata_path = current_path.parent.joinpath("../data/Ebola/genome_whole/input/metadata.csv")
blosum_path = current_path.parent.joinpath("../bin/blosum80.mat")
tp = TaskParameters(running_time="",
multialignment_file_path=multialignment_path,
multialignment_format="MAF",
datatype="N",
metadata_file_path=metadata_path,
blosum_file_path=blosum_path,
output_path=output_dir_path,
output_po=False,
output_fasta=False,
output_with_nodes=False,
verbose=False,
raw_maf=False,
fasta_provider='FromNCBI',
cache=True,
missing_base_symbol="",
fasta_source_file=None,
consensus_type="",
hbmin=0.8,
max_cutoff_option="MAX2",
search_range=None,
node_cutoff_option="NODE3",
multiplier=None,
stop=stop,
p=p)
fasta_provider = fp_ncbi.FromNCBI(use_cache=True)
multialignment_content = pathtools.get_file_content_stringio(multialignment_path)
multialignment = inp.Maf(file_content=multialignment_content, filename=multialignment_path)
metadata_content = pathtools.get_file_content_stringio(metadata_path)
metadata = inp.MetadataCSV(filecontent=metadata_content, filename=metadata_path)
poagraph, dagmaf = Poagraph.build_from_dagmaf(multialignment, fasta_provider, metadata)
blosum_content = pathtools.get_file_content_stringio(path=blosum_path)
blosum = cinp.Blosum(blosum_content, blosum_path)
return poagraph, tree_generator.get_consensus_tree(poagraph,
blosum,
consensus_output_dir,
cinp.Stop(stop),
cinp.P(p),
MAX2(),
NODE3(),
False)
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_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_2_no_seqid(self):
csv_path = self.csv_files_dir.joinpath("test_2_no_seqid.csv")
csv_content = pathtools.get_file_content_stringio(csv_path)
with self.assertRaises(Exception) as err:
_ = msa.MetadataCSV(csv_content, csv_path)
self.assertEqual(f"No \'seqid\' column in metadata csv.",
str(err.exception))
def test_3_empty_file(self):
csv_path = self.csv_files_dir.joinpath("test_3_empty_file.csv")
csv_content = pathtools.get_file_content_stringio(csv_path)
with self.assertRaises(Exception) as err:
_ = msa.MetadataCSV(csv_content, csv_path)
self.assertEqual(f"Empty csv file.", str(err.exception))
def setUp(self):
metadata_path = Path(__file__).parent.joinpath(
"../seq_metadata.csv").resolve()
self.metadatacsv = msa.MetadataCSV(
pathtools.get_file_content_stringio(metadata_path), metadata_path)
self.po_files_dir = Path(__file__).parent.joinpath(
"po_files").resolve()
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 setUp(self):
metadata_path = Path(__file__).parent.joinpath(
"../seq_metadata.csv").resolve()
self.metadatacsv = msa.MetadataCSV(
pathtools.get_file_content_stringio(metadata_path), metadata_path)
self.maf_files_dir = Path(__file__).parent.joinpath(
"maf_files_with_gaps").resolve()
self.missing_n = missings.MissingBase()
def get_default_blosum():
"""Returns default blosum file: Blosum80.mat"""
pangtreebuild_dir = Path(__file__).parent.parent
default_blosum_path = pathtools.get_child_path(
pangtreebuild_dir, "affinity_tree/bin/blosum80.mat")
blosum_content = pathtools.get_file_content_stringio(default_blosum_path)
return at_params.Blosum(blosum_content, default_blosum_path)
def setUp(self):
metadata_path = Path(__file__).parent.joinpath(
"../seq_metadata.csv").resolve()
self.metadatacsv = msa.MetadataCSV(
pathtools.get_file_content_stringio(metadata_path), metadata_path)
self.maf_files_dir = Path(__file__).parent.joinpath(
"maf_files_with_gaps").resolve()
self.fasta_provider = DAGMaf2PoagraphFakeFastaProviderTests.FakeFastaProvider(
)
def test_7_not_unique_seqids(self):
csv_path = self.csv_files_dir.joinpath("test_7_not_unique_seqids.csv")
csv_content = pathtools.get_file_content_stringio(csv_path)
with self.assertRaises(Exception) as err:
_ = msa.MetadataCSV(csv_content, csv_path)
self.assertEqual(
"Repeated values in seqid column in metadata file. Make them unique.",
str(err.exception))
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_incorrect_commas_number(self):
csv_path = self.csv_files_dir.joinpath(
"test_6_incorrect_commas_number.csv")
csv_content = pathtools.get_file_content_stringio(csv_path)
with self.assertRaises(Exception) as err:
_ = msa.MetadataCSV(csv_content, csv_path)
self.assertEqual(
"CSV metadata error. Different number of columns in line 0 than in header line.",
str(err.exception))
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_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_9_get_seqids(self):
metadata_path = self.csv_files_dir.joinpath("test_1_correct.csv")
csv_content = pathtools.get_file_content_stringio(metadata_path)
expected_seqids = [
msa.SequenceID('s1'),
msa.SequenceID('s2'),
msa.SequenceID('s3')
]
m = msa.MetadataCSV(csv_content, metadata_path)
actual_seqids = m.get_all_sequences_ids()
self.assertEqual(expected_seqids, actual_seqids)
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 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_4_seqid_is_last(self):
metadata_path = self.csv_files_dir.joinpath("test_4_seqid_is_last.csv")
csv_content = pathtools.get_file_content_stringio(metadata_path)
expected_metadata = {
msa.SequenceID('s1'): {
'name': 'sequence1',
'group': 'A'
},
msa.SequenceID('s2'): {
'name': 'sequence2',
'group': 'B'
},
msa.SequenceID('s3'): {
'name': 'sequence3',
'group': 'B'
}
}
m = msa.MetadataCSV(csv_content, metadata_path)
actual_metadata = m.metadata
self.assertEqual(expected_metadata, actual_metadata)
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 setUp(self):
metadata_path = Path(__file__).parent.joinpath("../seq_metadata.csv").resolve()
self.metadatacsv = msa.MetadataCSV(pathtools.get_file_content_stringio(metadata_path), metadata_path)
self.maf_files_dir = Path(__file__).parent.joinpath("maf_files_with_cycles_or_reversion").resolve()
self.fasta_provider = missings.ConstBaseProvider(missings.MissingBase())
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)
def get_default_blosum():
"""Returns default blosum file: Blosum80.mat"""
parent_dir = Path(os.path.dirname(os.path.abspath(__file__)) + '/')
default_blosum_path = pathtools.get_child_path(parent_dir, "../../bin/blosum80.mat")
blosum_content = pathtools.get_file_content_stringio(default_blosum_path)
return Blosum(blosum_content, default_blosum_path)
