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"""Test model annotations in SBML format."""
from pathlib import Path
from typing import TYPE_CHECKING
from cobra.io import read_sbml_model, write_sbml_model
if TYPE_CHECKING:
from cobra import Model
def _check_sbml_annotations(model: "Model") -> None:
"""Check the annotations from the annotation.xml.
Parameters
----------
model : cobra.Model
The model to check annotations for.
"""
assert model is not None
# model annotation
# {'bigg.model': 'e_coli_core', 'doi': '10.1128/ecosalplus.10.2.1',
# 'taxonomy': '511145'}
annotation = model.annotation
assert annotation is not None
assert len(annotation) == 3
for key in ["bigg.model", "doi", "taxonomy"]:
assert key in annotation
assert annotation["bigg.model"] == "e_coli_core"
assert annotation["doi"] == "10.1128/ecosalplus.10.2.1"
assert annotation["taxonomy"] == "511145"
# gene annotation
# {'asap': 'ABE-0006162', 'ncbigene': '946368', 'uniprot': 'P33221',
# 'ncbiprotein': 'gi:16129802', 'ecogene': 'EG11809'}
annotation = model.genes.G1.annotation
assert len(annotation) == 5
for key in ["asap", "ncbigene", "uniprot", "ncbiprotein", "ecogene"]:
assert key in annotation
assert annotation["asap"] == "ABE-0006162"
assert annotation["ncbigene"] == "946368"
assert annotation["uniprot"] == "P33221"
assert annotation["ncbiprotein"] == "16129802"
assert annotation["ecogene"] == "EG11809"
# compartment annotation
# FIXME: add tests with first class compartment model
# annotation = model.compartments.c.annotation
# assert len(annotation) == 1
# for key in ["bigg.compartment"]:
# assert key in annotation
# assert annotation["bigg.compartment"] == "c"
# metabolite/species annotation
# {'inchi': 'InChI=1S/C3H8O2/c1-3(5)2-4/h3-5H,2H2,1H3/t3-/m0/s1',
# 'bigg.metabolite': '13dpg', 'chebi': ['CHEBI:11881', 'CHEBI:16001',
# 'CHEBI:1658', 'CHEBI:20189', 'CHEBI:57604'],
# 'metanetx.chemical': 'MNXM261',
# 'kegg.compound': ['C00236', 'C02917'],
# 'seed.compound': 'cpd00203', 'hmdb': ['HMDB62758', 'HMDB06213'],
# 'biocyc': 'META:DPG'}
annotation = model.metabolites.A.annotation
for key in [
"inchi",
"bigg.metabolite",
"chebi",
"metanetx.chemical",
"kegg.compound",
"seed.compound",
"hmdb",
"biocyc",
]:
assert key in annotation
assert (
annotation["inchi"] == "InChI=1S/C3H8O2/c1-3(5)2-4/h3-5H,2H2,1H3/t3-/m0/s1"
) # noqa: E501
# reaction annotation
# {'kegg.reaction': 'R00228', 'sbo': 'SBO:0000375',
# 'ec-code': '1.2.1.10', 'rhea': ['23288', '23289', '23290', '23291'],
# 'metanetx.reaction': 'MNXR95210', 'bigg.reaction': 'ACALD',
# 'biocyc': 'META:ACETALD-DEHYDROG-RXN'}
annotation = model.reactions.R1.annotation
for key in [
"kegg.reaction",
"sbo",
"ec-code",
"rhea",
"metanetx.reaction",
"bigg.reaction",
"biocyc",
]:
assert key in annotation
assert annotation["biocyc"] == "META:ACETALD-DEHYDROG-RXN"
def test_read_sbml_annotations(data_directory: Path) -> None:
"""Test reading and writing annotations.
data_directory : pathlib.Path
The path to the test data directory.
"""
with open(data_directory / "annotation.xml", "r") as f_in:
model1 = read_sbml_model(f_in)
_check_sbml_annotations(model1)
def test_read_write_sbml_annotations(data_directory: Path, tmp_path: Path) -> None:
"""Test reading and writing annotations.
data_directory : pathlib.Path
The path to the test data directory.
tmp_path : pathlib.Path
The path to the temporary test assets store.
"""
with open(data_directory / "annotation.xml", "r") as f_in:
model1 = read_sbml_model(f_in)
sbml_path = tmp_path / "test.xml"
with open(sbml_path, "w") as f_out:
write_sbml_model(model1, f_out)
with open(sbml_path, "r") as f_in:
model2 = read_sbml_model(f_in)
_check_sbml_annotations(model2)
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