def test_6_repeated_sequences(self):
fasta_path = self.fasta_dir.joinpath("test_6_repeated_sequences.fasta")
with self.assertRaises(Exception) as exp:
_ = missings.FromFile(Path(fasta_path))
expected_message = "Incorrect fasta provided: sequences IDs are not unique."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_4_empty_sequence(self):
fasta_path = self.fasta_dir.joinpath("test_4_empty_sequence.fasta")
with self.assertRaises(Exception) as exp:
_ = missings.FromFile(Path(fasta_path))
expected_message = "Empty sequence in FASTA. Provide the sequence or remove its header."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_5_empty_fasta(self):
fasta_path = self.fasta_dir.joinpath("test_5_empty_fasta.fasta")
with self.assertRaises(Exception) as exp:
_ = missings.FromFile(Path(fasta_path))
expected_message = "No sequences in zipped fastas or incorrect zipped files."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_6_empty_zip(self):
fasta_path = self.fasta_dir.joinpath("test_6_empty_zip.zip")
with self.assertRaises(Exception) as exp:
_ = missings.FromFile(Path(fasta_path))
expected_message = "Incorrect zip fasta source."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_1_one_sequence(self):
fasta_path = self.fasta_dir.joinpath("test_1_one_sequence.fasta")
fasta_provider = missings.FromFile(Path(fasta_path))
sequence_id = msa.SequenceID("seq1")
expected_sequence = self.read_sequence(fasta_path)
self.raise_error_if_unequal(sequence_id,
expected_sequence,
fasta_provider)
def test_1_one_sequence_one_file_in_zip(self):
fasta_path = self.fasta_dir.joinpath(
"test_1_one_sequence_one_file_in_zip.zip")
fasta_provider = missings.FromFile(Path(fasta_path))
sequence_id = msa.SequenceID("seq1")
expected_sequence = "ACTGGGTGGGA"
self.raise_error_if_unequal(sequence_id, expected_sequence,
fasta_provider)
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_three_sequences_in_two_files_in_zip(self):
fasta_path = self.fasta_dir.joinpath(
"test_2_three_sequences_in_two_files_in_zip.zip")
fasta_provider = missings.FromFile(Path(fasta_path))
sequence_id_1 = msa.SequenceID("seq1")
self.raise_error_if_unequal(sequence_id_1, "ACTGGGTGGGA",
fasta_provider)
sequence_id_2 = msa.SequenceID("seq2")
self.raise_error_if_unequal(sequence_id_2, "AA", fasta_provider)
sequence_id_3 = msa.SequenceID("seq3")
self.raise_error_if_unequal(sequence_id_3, "GT", fasta_provider)
def resolve_fasta_provider(args: argparse.Namespace) -> \
missings.FastaProvider:
"""Returns fasta provider based on parsed arguments."""
if args.fasta_provider is None:
if args.missing_symbol is None:
return missings.ConstBaseProvider(missings.MissingBase())
else:
return missings.ConstBaseProvider(args.missing_symbol)
elif args.fasta_provider == 'ncbi':
use_cache = args.cache if args.cache else False
return missings.FromNCBI(use_cache)
elif args.fasta_provider == 'file':
if args.fasta_path is None:
raise Exception("""Fasta file source must be specified.
It must be provided when fasta source
is \'local\'.""")
return missings.FromFile(args.fasta_path)
else:
raise Exception("""Not known fasta provider.
Should be \'ncbi\' or \'file\' or None.
Cannot build graph.""")
