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_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 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_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)
