def test_execute_action_deletion(self):
action = "deletion"
# Delete Gene
target = Mock()
gene = Gene()
self.widget.execute_action((target, action, gene))
target.remove_child.assert_called_once_with(gene)
# Delete GeneGroup
target = Mock()
gene_group = GeneGroup()
gene_group.delete_children = Mock()
self.widget.execute_action((target, action, gene_group))
target.remove_child.assert_called_once_with(gene_group)
assert gene_group.delete_children.called is False
# Check that children are deleted if genegroup has only one parent
target = Mock()
gene_group = GeneGroup()
gene_group.add_parent(self.reaction)
gene_group.delete_children = Mock()
self.widget.execute_action((target, action, gene_group))
target.remove_child.assert_called_once_with(gene_group)
assert gene_group.delete_children.called is True
def test_nested_genegroups_with_gene(self):
genegroup1 = GeneGroup()
genegroup2 = GeneGroup()
gene = Gene("gene id")
genegroup1.add_child(genegroup2)
genegroup2.add_child(gene)
assert genegroup1.gem_reaction_rule == gene.id
gene2 = Gene("gene2 id")
genegroup2.add_child(gene2)
assert genegroup1.gem_reaction_rule == "("+gene.id+" and "+gene2.id+")"
def test_gene_and_gene_group(self):
gene1 = Gene("gene 1")
gene2 = Gene("gene 2")
gene3 = Gene("gene 3")
genegroup1 = GeneGroup(type="and")
genegroup2 = GeneGroup(type="or")
reaction = Reaction()
reaction.add_child(genegroup1)
genegroup1.add_child(gene1)
genegroup1.add_child(genegroup2)
genegroup2.add_child(gene2)
assert reaction.gene_reaction_rule == gene1.id+" and "+gene2.id
genegroup2.add_child(gene3)
assert reaction.gene_reaction_rule == gene1.id+" and ("+gene2.id+" or "+gene3.id+")"
def _parse_gene_xml_tree(node, reaction, genes):
""" Parse the gene tree as saved in an sbml file with fbc package """
# Check that
if node.tag == fbc_geneProductAssociation:
top_level_child = _parse_gene_xml_tree(node.getchildren()[0], reaction,
genes)
reaction.add_child(top_level_child)
elif node.tag in (fbc_and, fbc_or):
gene_group = GeneGroup(id=node.get(ge_id),
type="and" if node.tag == fbc_and else "or")
for child in node.getchildren():
child_object = _parse_gene_xml_tree(child, reaction, genes)
gene_group.add_child(child_object)
return gene_group
elif node.tag == fbc_geneProductRef:
gene_id = clip(node.attrib[fbc_geneProduct], "G_")
# Resubstitute dots
gene_id = gene_id.replace(SBML_DOT, ".")
try:
return genes.get_by_id(gene_id)
except KeyError:
new_gene = Gene(id=gene_id, name=gene_id)
genes.append(new_gene)
warn("Gene {0} not found in gene list. New gene created!".format(
gene_id))
return new_gene
else:
raise TypeError("Unknown node.tag {0} at line {1}".format(
node.tag, node.sourceline))
def test_genegroup_enabled_different_genes(self):
group1 = GeneGroup()
gene1 = Gene()
gene1.functional = False
group1.add_child(gene1)
group1.type = "and"
assert group1.functional is False
group1.type = "or"
assert group1.functional is False
# Add second functional gene
gene2 = Gene()
gene2.functional = True
group1.add_child(gene2)
group1.type = "and"
assert group1.functional is False
group1.type = "or"
assert group1.functional is True
group1.type = "unknown"
with pytest.raises(ValueError):
group1.functional
def test_reaction_is_disabled_with_gene_in_and_group(self):
reaction = Reaction()
genegroup = GeneGroup(type="and")
reaction.add_child(genegroup)
gene = Gene()
genegroup.add_child(gene)
gene.functional = False
assert reaction.functional is False
def test_removal_of_nested_or_groups(self):
reaction = Reaction("r1")
gene_group1 = GeneGroup(type="or")
gene_group2 = GeneGroup(type="or")
gene1 = Gene("g1")
gene2 = Gene("g2")
gene3 = Gene("g3")
gene_group1.add_child(gene1)
for x in (gene2, gene3):
gene_group2.add_child(x)
gene_group1.add_child(gene_group2)
reaction.add_child(gene_group1)
assert reaction.genes == set([gene1, gene2, gene3])
prune_gene_tree(reaction)
assert reaction.genes == set([gene1, gene2, gene3])
assert not gene_group2._children
assert not gene_group2._parents
def test_two_genes_one_gene_group(self, reaction):
gene1 = Gene("test 1")
gene2 = Gene("test 2")
group = GeneGroup(type="and")
group.add_child(gene1)
group.add_child(gene2)
reaction.add_child(group)
assert reaction.gene_reaction_rule == gene1.id + " and " + gene2.id
group.type = "or"
assert reaction.gene_reaction_rule == gene1.id + " or " + gene2.id
def test_removal_empty_genegroup(self):
reaction = Reaction("r1")
gene_group = GeneGroup()
reaction.add_child(gene_group)
assert gene_group in reaction._children
assert reaction in gene_group._parents
prune_gene_tree(reaction)
assert gene_group not in reaction._children
assert reaction not in gene_group._parents
class TestGene:
def test_default_values(self):
gene = Gene()
assert gene.id == ""
assert gene.name == ""
assert gene.genome == ""
assert gene.annotation == set()
assert gene.functional is True
@pytest.mark.parametrize("child", [Gene(), Reaction(), GeneGroup()])
def test_gene_add_child(self, child):
gene = Gene()
with pytest.raises(NotImplementedError):
gene.add_child(child)
@pytest.mark.parametrize("child", [Gene(), Reaction(), GeneGroup()])
def test_gene_remove_child(self, child):
gene = Gene()
with pytest.raises(NotImplementedError):
gene.remove_child(child)
def add_genegroup(self):
""" Buffer the addition of a genegroup to the genegroup and change the model"""
# Get current item
table_item, model_item = self.get_selected_item()
new_group = GeneGroup()
new_item = LinkedItem(text=str(new_group.type).upper(), link=new_group)
new_item.setEditable(False)
table_item.appendRow(new_item)
# Buffer the function call for when user accepts dialog
self.cached_actions.append((model_item, "addition", new_group))
self.changed.emit()
def test_multiple_nested(self):
reaction = Reaction()
parent = reaction
for _ in range(5):
genegroup = GeneGroup()
parent.add_child(genegroup)
parent = genegroup
gene = Gene("Gene id")
parent.add_child(gene)
assert reaction.gene_reaction_rule == gene.id
gene2 = Gene("Gene 2")
parent.add_child(gene2)
assert reaction.gene_reaction_rule == "(" + gene.id+" and "+gene2.id+")"
def test_context_menu_genegroup(self):
reaction = Reaction()
model = Model()
genegroup = GeneGroup()
self.widget.set_item(reaction, model)
self.widget.geneTable.appendRow(LinkedItem("test", genegroup))
assert self.widget.geneTable.rowCount() == 1
index = self.widget.geneTable.item(0, 0).index()
self.widget.geneView.setCurrentIndex(index)
assert self.widget.get_selected_item()[1] is genegroup
menu = self.widget.show_gene_contextmenu(QtCore.QPoint())
assert self.widget.delete_genegroup_action in menu.actions()
assert self.widget.add_gene_action in menu.actions()
assert self.widget.add_genegroup_action in menu.actions()
def merge_reactions(list_of_reactions, base_reaction):
""" Merge duplicated reactions
Parameters
----------
list_of_reactions: list, list of reactions that should be merged
base_reaction: GEMEditor.model.classes.cobra.Reaction, Reaction to keep
Returns
-------
"""
# Move all genes of the base reaction to new gene group
temp_children = []
base_children = extract_genes_from_reaction(base_reaction)
if base_children is not None:
temp_children.append(base_children)
merged_reactions = defaultdict(list)
for reaction in list_of_reactions:
if reaction is not base_reaction:
# Add annotations
base_reaction.annotation.update(reaction.annotation)
# Add genes
genes = extract_genes_from_reaction(reaction)
if genes is not None:
temp_children.append(genes)
# Move evidences
for evidence in reaction.evidences:
evidence.substitute_item(reaction, base_reaction)
# Mark reaction for deletion
merged_reactions[reaction.model].append(reaction)
# Remove reactions
for model, delete_reactions in merged_reactions.items():
if model:
model.gem_remove_reactions(delete_reactions)
# Add new genes to base reaction
if len(temp_children) > 1:
combined_genes = GeneGroup(type="or")
for element in temp_children:
combined_genes.add_child(element)
base_reaction.add_child(combined_genes)
elif len(temp_children) == 1:
base_reaction.add_child(temp_children[0])
def test_removal_of_genegroup_with_one_child(self, type):
reaction = Reaction("r1")
gene_group = GeneGroup(type=type)
gene = Gene()
reaction.add_child(gene_group)
gene_group.add_child(gene)
assert gene_group in reaction._children
assert reaction in gene_group._parents
assert gene in reaction.genes
prune_gene_tree(reaction)
assert gene_group not in reaction._children
assert reaction not in gene_group._parents
assert gene in reaction.genes
def test_execute_action_addition(self):
action = "addition"
# Add Gene
target = Mock()
gene = Gene()
self.widget.execute_action((target, action, gene))
target.add_child.assert_called_once_with(gene)
# Add GeneGroup
target = Mock()
gene_group = GeneGroup()
self.widget.execute_action((target, action, gene_group))
target.add_child.assert_called_once_with(gene_group)
def setup_complete_model(self):
self.model = Model("model")
# Setup reaction1
self.metabolite = Metabolite("m1")
self.reaction = Reaction("r1")
self.gene = Gene("g1")
self.reaction.add_child(self.gene)
self.model.add_genes((self.gene,))
self.reaction.add_metabolites({self.metabolite: -1})
self.model.add_reactions((self.reaction,))
# Setup reaction2
self.metabolite2 = Metabolite("m2")
self.reaction2 = Reaction("r2")
self.gene2 = Gene("g2")
self.genegroup = GeneGroup()
self.genegroup.add_child(self.gene2)
self.reaction2.add_child(self.genegroup)
self.model.add_genes((self.gene2,))
self.reaction2.add_metabolites({self.metabolite2: 1})
self.model.add_reactions((self.reaction2,))
# Setup evidences
self.evidence = Evidence(assertion="Catalyzes")
self.evidence.set_entity(self.gene)
self.evidence.set_target(self.reaction)
self.reference = Reference()
self.model.add_reference(self.reference)
self.evidence.add_reference(self.reference)
self.model.add_evidence(self.evidence)
# Setup test case
self.testcase = ModelTest()
reaction_setting = ReactionSetting(self.reaction, 1000., -1000., 0.)
gene_setting = GeneSetting(gene=self.gene2, activity=False)
outcome = Outcome(self.reaction2, 0., "greater")
self.testcase.add_outcome(outcome)
self.testcase.add_setting(gene_setting)
self.testcase.add_setting(reaction_setting)
self.model.add_test(self.testcase)
self.reference2 = Reference()
self.model.add_reference(self.reference2)
self.testcase.add_reference(self.reference2)
self.model.setup_tables()
def test_delete_children(self):
reaction = Reaction()
reaction2 = Reaction()
genegroup = GeneGroup()
gene = Gene()
reaction.add_child(genegroup)
reaction2.add_child(genegroup)
genegroup.add_child(gene)
assert genegroup in reaction._children
assert reaction in genegroup._parents
assert genegroup in reaction2._children
assert reaction2 in genegroup._parents
assert gene in genegroup._children
assert genegroup in gene._parents
reaction.delete_children()
assert genegroup not in reaction._children
assert reaction not in genegroup._parents
assert gene not in genegroup._children
assert genegroup not in gene._parents
assert genegroup in reaction2._children
assert reaction2 in genegroup._parents
def extract_genes_from_reaction(reaction):
""" Remove all genes from a reaction an get a new genegroup from it
Parameters
----------
reaction: GEMEditor.model.classes.cobra.Reaction
Returns
-------
"""
if not reaction._children:
return None
elif len(reaction._children) == 1:
child = list(reaction._children)[0]
child.remove_parent(reaction, all=False)
return child
new_genegroup = GeneGroup(type="or")
for element in reaction._children:
element.remove_parent(reaction, all=False)
element.add_parent(new_genegroup)
return new_genegroup
class TestReaction:
@pytest.fixture()
def setup_item(self):
self.test_id = "test_id"
self.test_name = "test_name"
self.test_upper_bound = 1000.
self.test_lower_bound = -1000.
self.reaction = Reaction(id=self.test_id,
name=self.test_name,
lower_bound=self.test_lower_bound,
upper_bound=self.test_upper_bound)
@pytest.mark.usefixtures("setup_item")
def test_setup_item(self):
assert self.reaction.id == self.test_id
assert self.reaction.name == self.test_name
assert self.reaction.upper_bound == self.test_upper_bound
assert self.reaction.lower_bound == self.test_lower_bound
assert self.reaction._model is None
def test_empty_reaction_setup(self):
reaction = Reaction()
assert reaction.id == ""
assert reaction.name == ""
assert reaction.subsystem == ""
assert reaction.lower_bound == 0.
assert reaction.upper_bound == 1000.
assert reaction.comment == ""
assert reaction.annotation == set()
assert reaction.model is None
assert len(reaction._children) == 0
def test_none_reaction_setup(self):
reaction = Reaction(id=None,
name=None,
subsystem=None,
lower_bound=None,
upper_bound=None,
comment=None)
assert reaction.id == ""
assert reaction.name == ""
assert reaction.subsystem == ""
assert reaction.lower_bound == 0.
assert reaction.upper_bound == 1000.
assert reaction.comment == ""
assert len(reaction._children) == 0
@pytest.mark.usefixtures("setup_item")
@pytest.mark.parametrize("lower_bound,upper_bound,objective", [(0., 1000., 0.),
(-1000., 1000., 1.),
(-1000., 0., 20.),
(0., 0., 0.)])
def test_get_setting(self, lower_bound, upper_bound, objective):
self.reaction.upper_bound = upper_bound
self.reaction.lower_bound = lower_bound
setting = self.reaction.get_setting()
assert setting.reaction is self.reaction
assert setting.upper_bound == upper_bound
assert setting.lower_bound == lower_bound
def test_gene_addition(self):
reaction = Reaction("reaction_id")
gene = Gene("gene_id")
reaction.add_child(gene)
assert gene in reaction.genes
assert reaction in gene.reactions
def test_reaction_gene_addition(self, ex_empty_reaction):
test_gene = Gene(id="test", name="test")
# Check addition
ex_empty_reaction.add_child(test_gene)
assert test_gene in ex_empty_reaction._children
assert ex_empty_reaction in test_gene._parents
# Check removal
ex_empty_reaction.remove_child(test_gene)
assert test_gene not in ex_empty_reaction._children
assert ex_empty_reaction not in test_gene._parents
def test_reaction_genegroup_addition(self):
reaction = ex_empty_reaction()
genegroup = ex_empty_geneGroup()
# Check addition and references
reaction.add_child(genegroup)
assert genegroup in reaction._children
assert reaction in genegroup._parents
# Check removal
reaction.remove_child(genegroup)
assert genegroup not in reaction._children
assert genegroup._parents == []
@pytest.mark.parametrize("parent", [Gene(), GeneGroup(), Reaction()])
def test_add_parent(self, parent):
reaction = Reaction()
with pytest.raises(NotImplementedError):
reaction.add_parent(parent)
@pytest.mark.parametrize("parent", [Gene(), GeneGroup(), Reaction()])
def test_remove_parent(self, parent):
reaction = Reaction()
with pytest.raises(NotImplementedError):
reaction.remove_parent(parent)
@pytest.mark.usefixtures("setup_item")
def test_reaction_subsystem_setting(self):
model = Model()
# Test subsystem setting while reaction not in model
new_subsystem1 = "New subsystem"
self.reaction.subsystem = new_subsystem1
assert self.reaction.subsystem == new_subsystem1
# Test that the subsystem is updated on the model
model.add_reactions([self.reaction])
assert model is self.reaction._model
assert len(model.subsystems) == 1
assert new_subsystem1 in model.subsystems
assert self.reaction in model.subsystems[new_subsystem1]
# Test that changing the subsystem is reflected in model.subsystems
new_subsystem2 = "Different Stubsystem"
self.reaction.subsystem = new_subsystem2
assert len(model.subsystems) == 1
assert new_subsystem2 in model.subsystems
assert self.reaction in model.subsystems[new_subsystem2]
def test_reaction_enabled_without_genes(self):
reaction = Reaction()
assert reaction.functional is True
def test_reaction_enabled_true_with_empty_genegroup(self):
reaction = Reaction()
genegroup = GeneGroup()
reaction.add_child(genegroup)
assert reaction.functional is True
def test_reaction_is_disabled_with_disabled_gene_only(self):
reaction = Reaction()
gene = Gene()
gene.functional = False
reaction.add_child(gene)
assert reaction.functional is False
def test_reaction_is_disabled_with_gene_in_or_group(self):
reaction = Reaction()
genegroup = GeneGroup(type="or")
reaction.add_child(genegroup)
gene = Gene()
genegroup.add_child(gene)
gene.functional = False
assert reaction.functional is False
def test_reaction_is_disabled_with_gene_in_and_group(self):
reaction = Reaction()
genegroup = GeneGroup(type="and")
reaction.add_child(genegroup)
gene = Gene()
genegroup.add_child(gene)
gene.functional = False
assert reaction.functional is False
def genegroup(self):
return GeneGroup()
def test_one_gene_genegroup(self):
gene = Gene("test 1")
genegroup = GeneGroup()
genegroup.add_child(gene)
assert genegroup.gem_reaction_rule == gene.id
def test_empty_gene_group_setup(self):
gene_group = GeneGroup()
assert gene_group.id
assert gene_group.type == "and"
def test_reaction_enabled_true_with_empty_genegroup(self):
reaction = Reaction()
genegroup = GeneGroup()
reaction.add_child(genegroup)
assert reaction.functional is True
def test_nested_genegroups_wo_gene(self):
genegroup1 = GeneGroup()
genegroup2 = GeneGroup()
genegroup1.add_child(genegroup2)
assert genegroup1.gem_reaction_rule == ""
def ex_empty_geneGroup():
return GeneGroup()
def test_genegroup_enabled_for_empty_group(self):
genegroup = GeneGroup()
assert genegroup.functional is None