def create_padmet_stat(species_name, padmet_file):
"""Extract reactions/pathways/compounds/genes from a padmet file.
Args:
species_name (str): species names
padmet_file (str): path to a padmet file
Returns
list: [species name, list of genes, list of reactions, list of reactions associated with genes, list of compounds, list of pathways]
"""
padmetSpec = PadmetSpec(padmet_file)
total_pwy_id = set()
total_cpd_id = set()
all_rxns = [node for node in padmetSpec.dicOfNode.values() if node.type == "reaction"]
all_genes = [node.id for node in padmetSpec.dicOfNode.values() if node.type == "gene"]
gene_associated_rxns = []
genes_with_rxns = []
rxns = []
for rxn_node in all_rxns:
total_cpd_id.update([rlt.id_out for rlt in padmetSpec.dicOfRelationIn[rxn_node.id] if rlt.type in ["consumes","produces"]])
pathways_ids = set([rlt.id_out for rlt in padmetSpec.dicOfRelationIn[rxn_node.id] if rlt.type == "is_in_pathway"])
rxns.append(rxn_node.id)
if any([rlt for rlt in padmetSpec.dicOfRelationIn[rxn_node.id] if rlt.type == "is_linked_to"]):
genes_with_rxns.extend([rlt.id_out for rlt in padmetSpec.dicOfRelationIn[rxn_node.id] if rlt.type == "is_linked_to"])
gene_associated_rxns.append(rxn_node.id)
total_pwy_id.update(pathways_ids)
all_pwys = [node_id for (node_id, node) in padmetSpec.dicOfNode.items() if node_id in total_pwy_id]
all_cpds = [node_id for (node_id, node) in padmetSpec.dicOfNode.items() if node_id in total_cpd_id]
genes_with_rxns = set(genes_with_rxns)
return [species_name, genes_with_rxns, rxns, gene_associated_rxns, all_cpds, all_pwys]
def test_sbml_to_padmet_cli():
subprocess.call([
'padmet', 'pgdb_to_padmet', '--pgdb', 'test_data/pgdb', '--output',
'test.padmet', '--extract-gene'
])
subprocess.call([
'padmet', 'sbmlGenerator', '--padmet', 'test.padmet', '--output',
'fabo.sbml', '--sbml_lvl', '3'
])
subprocess.call([
'padmet', 'sbml_to_padmet', '--sbml', 'fabo.sbml', '--padmetSpec',
'fabo.padmet'
])
fabo_padmet = PadmetSpec('fabo.padmet')
all_pwys, all_cpds, all_rxns, all_genes = extract_data_padmet(fabo_padmet)
assert all_pwys == []
assert set(FABO_RXNS).issubset(set(all_rxns))
assert set(FABO_CPDS).issubset(set(all_cpds))
assert set(FABO_GENES).issubset(set(all_genes))
os.remove('fabo.sbml')
os.remove('test.padmet')
os.remove('fabo.padmet')
def test_padmet_to_padmet_reversibility_cli():
"""
Test an issue encountered when a reaction is defined in a direction in one padmet.
And in another the same reaction is defined as reversible.
In old padmet this leads to the reaction having all of its reactants/products as reactants and also as products.
"""
# Read padmet file
subprocess.call([
'padmet', 'padmet_to_padmet', '--to_add', 'test_data/padmet',
'--output', 'fabo.padmet'
])
expected_padmet = PadmetSpec('fabo.padmet')
reactants = [
rlt.id_out
for rlt in expected_padmet.dicOfRelationIn['ENOYL-COA-HYDRAT-RXN']
if rlt.type in ['consumes']
]
products = [
rlt.id_out
for rlt in expected_padmet.dicOfRelationIn['ENOYL-COA-HYDRAT-RXN']
if rlt.type in ['produces']
]
assert sorted(reactants) == [
'TRANS-D2-ENOYL-COA', 'WATER'
] or sorted(products) == ['TRANS-D2-ENOYL-COA', 'WATER']
assert sorted(products) == [
'L-3-HYDROXYACYL-COA'
] or sorted(reactants) == ['L-3-HYDROXYACYL-COA']
os.remove('fabo.padmet')
def test_padmet_to_padmet():
# Using inpu data, create 2 padmets and delete one reaction in each.
fabo_1_padmetSpec = from_pgdb_to_padmet('test_data/pgdb',
extract_gene=True)
fabo_1_padmetSpec.delNode('ACYLCOASYN-RXN')
fabo_1_padmetSpec.generateFile('fabo_1.padmet')
_, _, all_rxns, _ = extract_data_padmet(fabo_1_padmetSpec)
assert not set(FABO_RXNS).issubset(set(all_rxns))
fabo_2_padmetSpec = from_pgdb_to_padmet('test_data/pgdb',
extract_gene=True)
fabo_2_padmetSpec.delNode('ACYLCOADEHYDROG-RXN')
fabo_2_padmetSpec.generateFile('fabo_2.padmet')
_, _, all_rxns, _ = extract_data_padmet(fabo_2_padmetSpec)
assert not set(FABO_RXNS).issubset(set(all_rxns))
# By merging them we should retrieve the two deleted reactions
padmet_to_padmet('fabo_1.padmet,fabo_2.padmet', 'fabo.padmet')
expected_padmet = PadmetSpec('fabo.padmet')
_, _, all_rxns, _ = extract_data_padmet(expected_padmet)
assert set(FABO_RXNS).issubset(set(all_rxns))
os.remove('fabo_1.padmet')
os.remove('fabo_2.padmet')
os.remove('fabo.padmet')
def test_sbml_to_padmet():
fabo_padmetSpec = from_pgdb_to_padmet('test_data/pgdb', extract_gene=True)
padmet_to_sbml(fabo_padmetSpec, 'fabo.sbml')
sbml_to_padmetSpec('fabo.sbml', 'fabo.padmet')
fabo_padmet = PadmetSpec('fabo.padmet')
all_pwys, all_cpds, all_rxns, all_genes = extract_data_padmet(fabo_padmet)
assert all_pwys == []
assert set(FABO_RXNS).issubset(set(all_rxns))
assert set(FABO_CPDS).issubset(set(all_cpds))
assert set(FABO_GENES).issubset(set(all_genes))
os.remove('fabo.sbml')
os.remove('fabo.padmet')
def test_pgdb_to_padmet_without_genes_cli():
subprocess.call([
'padmet', 'pgdb_to_padmet', '--pgdb', 'test_data/pgdb', '--output',
'test.padmet'
])
test_padmetSpec = PadmetSpec('test.padmet')
all_pwys, all_cpds, all_rxns, all_genes = extract_data_padmet(
test_padmetSpec)
assert all_pwys == FABO_PWYS
assert set(FABO_RXNS).issubset(set(all_rxns))
assert set(FABO_CPDS).issubset(set(all_cpds))
assert all_genes == []
os.remove('test.padmet')
def test_sbmlGenerator_cli():
subprocess.call([
'padmet', 'pgdb_to_padmet', '--pgdb', 'test_data/pgdb', '--output',
'test.padmet', '--extract-gene'
])
fabo_padmetSpec = PadmetSpec('test.padmet')
subprocess.call([
'padmet', 'sbmlGenerator', '--padmet', 'test.padmet', '--output',
'fabo.sbml', '--sbml_lvl', '3'
])
genes, id_compounds, id_reactions = extract_data_sbml('fabo.sbml')
assert set(FABO_RXNS).issubset(set(id_reactions))
assert set(FABO_CPDS).issubset(set(id_compounds))
assert set(FABO_GENES).issubset(set(genes))
os.remove('test.padmet')
os.remove('fabo.sbml')
def test_pgdb_to_padmet_no_orphan_with_genes_cli():
subprocess.call([
'padmet', 'pgdb_to_padmet', '--pgdb', 'test_data/pgdb', '--output',
'test.padmet', '--extract-gene', '--no-orphan'
])
test_padmetSpec = PadmetSpec('test.padmet')
all_pwys, all_cpds, all_rxns, all_genes = extract_data_padmet(
test_padmetSpec)
assert all_pwys == FABO_PWYS
# 2.3.1.49-RXN is added as it has no association with genes
assert '2.3.1.49-RXN' not in all_rxns
assert set(FABO_CPDS).issubset(set(all_cpds))
# b24589 is a manually added genes without association to a reaction
assert 'b24589' not in all_genes
os.remove('test.padmet')
def test_pgdb_to_padmet_cli():
subprocess.call([
'padmet', 'pgdb_to_padmet', '--pgdb', 'test_data/pgdb', '--output',
'test.padmet', '--extract-gene'
])
test_padmetSpec = PadmetSpec('test.padmet')
all_pwys, all_cpds, all_rxns, all_genes = extract_data_padmet(
test_padmetSpec)
assert all_pwys == FABO_PWYS
assert test_padmetSpec.dicOfNode['FAO-PWY'].misc['COMMON-NAME'][
0] == 'fatty acid β-oxidation I - (generic)'
assert set(FABO_RXNS).issubset(set(all_rxns))
assert set(FABO_CPDS).issubset(set(all_cpds))
assert set(FABO_GENES).issubset(set(all_genes))
os.remove('test.padmet')
def test_padmet_to_padmet_cli():
# Using inpu data, create 2 padmets and delete one reaction in each.
subprocess.call([
'padmet', 'pgdb_to_padmet', '--pgdb', 'test_data/pgdb', '--output',
'test.padmet', '--extract-gene'
])
fabo_1_padmetSpec = PadmetSpec('test.padmet')
fabo_1_padmetSpec.delNode('ACYLCOASYN-RXN')
fabo_1_padmetSpec.generateFile('fabo_1.padmet')
_, _, all_rxns, _ = extract_data_padmet(fabo_1_padmetSpec)
os.remove('test.padmet')
assert not set(FABO_RXNS).issubset(set(all_rxns))
subprocess.call([
'padmet', 'pgdb_to_padmet', '--pgdb', 'test_data/pgdb', '--output',
'test.padmet', '--extract-gene'
])
fabo_2_padmetSpec = PadmetSpec('test.padmet')
fabo_2_padmetSpec.delNode('ACYLCOADEHYDROG-RXN')
fabo_2_padmetSpec.generateFile('fabo_2.padmet')
_, _, all_rxns, _ = extract_data_padmet(fabo_2_padmetSpec)
os.remove('test.padmet')
assert not set(FABO_RXNS).issubset(set(all_rxns))
# By merging them we should retrieve the two deleted reactions
padmet_to_padmet('fabo_1.padmet,fabo_2.padmet', 'fabo.padmet')
subprocess.call([
'padmet', 'padmet_to_padmet', '--to_add',
'fabo_1.padmet,fabo_2.padmet', '--output', 'fabo.padmet'
])
expected_padmet = PadmetSpec('fabo.padmet')
_, _, all_rxns, _ = extract_data_padmet(expected_padmet)
assert set(FABO_RXNS).issubset(set(all_rxns))
os.remove('fabo_1.padmet')
os.remove('fabo_2.padmet')
os.remove('fabo.padmet')