def test_sbml_filter4(self):
f = "test/gene-filter-example-4.xml"
self.assertTrue(os.path.isfile(f), msg="cannot find test file")
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml(filter_species=["a"], filter_genes=["r"])
self.assertEqual(sbml.getNumErrors(), 0)
self.assertTrue("modelname" in sbml.getModel().getName())
self.assertTrue("modelid" in sbml.getModel().getId())
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 3)
self.assertEqual(len(net.reactions["r1"].consumed), 0)
self.assertEqual(len(net.reactions["r1"].produced), 1)
self.assertEqual(len(net.reactions["r1"].genes), 3)
self.assertEqual(len(net.reactions["r1"].genec), 3)
self.assertEqual(len(net.reactions["r2"].consumed), 1)
self.assertEqual(len(net.reactions["r2"].produced), 1)
self.assertEqual(len(net.reactions["r2"].genes), 2)
self.assertEqual(len(net.reactions["r2"].genec), 3)
self.assertEqual(len(net.reactions["r3"].consumed), 0)
self.assertEqual(len(net.reactions["r3"].produced), 1)
self.assertEqual(len(net.reactions["r3"].genes), 1)
self.assertEqual(len(net.reactions["r3"].genec), 0)
def test_implode_genes(self):
genes = [Gene('a')]
genes.append(GeneComplex(Gene('x')))
gc = GeneComplex()
gc.add_gene(Gene("b"))
gc.add_gene(Gene("c"))
genes.append(gc)
genes.append(Gene('sdkflj alskd2345 34lk5 w34knflk324'))
f = "test/gene-filter-example-3.xml"
gemtractor = GEMtractor(f)
self.assertEqual(
"((a) or (x) or (b and c) or (sdkflj alskd2345 34lk5 w34knflk324))",
gemtractor._implode_genes(genes))
def test_extract_from_notes(self):
f = "test/gene-filter-example-3.xml"
gemtractor = GEMtractor(f)
note = """
<html xmlns="http://www.w3.org/1999/xhtml"><p>GENE_ASSOCIATION: (a or (b and c) or d or (f and g and k) or (k and a))</p><p>GENE_LIST: whatever</p><p>SUBSYSTEM: Pyruvate Metabolism</p></html>
"""
self.assertEqual(
gemtractor._extract_genes_from_sbml_notes(note, "def"),
"(a or (b and c) or d or (f and g and k) or (k and a))")
note = """
<html xmlns="http://www.w3.org/1999/xhtml"><p>GENE_ASSOCIATION:(a or (b and c) or d or (f and g and k) or (k and a))</p><p>GENE_LIST: whatever</p><p>SUBSYSTEM: Pyruvate Metabolism</p></html>
"""
self.assertEqual(
gemtractor._extract_genes_from_sbml_notes(note, "def"),
"(a or (b and c) or d or (f and g and k) or (k and a))")
note = """
<html xmlns="http://www.w3.org/1999/xhtml"><p>GENE_ASSOCIATION:a or b</p><p>GENEsadfsdflism</p></html>
"""
self.assertEqual(
gemtractor._extract_genes_from_sbml_notes(note, "def"), "a or b")
note = """
<html xmlns="http://www.w3.org/1999/xhtml"><p>GENE_ASSOCIATION:gene</p><p>GENEsadfsdflism</p></html>
"""
self.assertEqual(
gemtractor._extract_genes_from_sbml_notes(note, "def"), "gene")
note = """
<html xmlns="http://www.w3.org/1999/xhtml"><p>GENE_ASSOCIATION: gene </p><p>GENEsadfsdflism</p></html>
"""
self.assertEqual(
gemtractor._extract_genes_from_sbml_notes(note, "def"), "gene")
note = """
<html xmlns="http://www.w3.org/1999/xhtml"><p></p><p>GENEsadfsdflism</p></html>
"""
self.assertEqual(
gemtractor._extract_genes_from_sbml_notes(note, "def"), "def")
def test_parse_expression(self):
f = "test/gene-filter-example-3.xml"
gemtractor = GEMtractor(f)
expr = gemtractor._unfold_complex_expression(
gemtractor._parse_expression("something"))
self.assertEqual(len(expr), 1)
self.assertEqual(len(expr[0].genes), 1)
self.assertEqual(next(iter(expr[0].genes)).identifier, "something")
expr = gemtractor._unfold_complex_expression(
gemtractor._parse_expression(
"a or ((b and c) or (d and e and f)) or (g and h) or (i or j)")
)
self.assertEqual(len(expr), 6)
self.assertEqual(len(expr[0].genes), 1)
self.assertEqual(next(iter(expr[0].genes)).identifier, "a")
self.assertEqual(len(expr[1].genes), 2)
self.assertTrue(next(iter(expr[1].genes)).identifier, "b")
self.assertTrue(next(iter(expr[1].genes)).identifier, "c")
self.assertEqual(len(expr[2].genes), 3)
self.assertTrue(next(iter(expr[2].genes)).identifier, "d")
self.assertTrue(next(iter(expr[3].genes)).identifier, "e")
self.assertTrue(next(iter(expr[3].genes)).identifier, "f")
self.assertEqual(len(expr[3].genes), 2)
self.assertTrue(next(iter(expr[3].genes)).identifier, "g")
self.assertTrue(next(iter(expr[3].genes)).identifier, "h")
self.assertEqual(len(expr[4].genes), 1)
self.assertEqual(next(iter(expr[4].genes)).identifier, "i")
self.assertEqual(len(expr[5].genes), 1)
self.assertEqual(next(iter(expr[5].genes)).identifier, "j")
expr = gemtractor._unfold_complex_expression(
gemtractor._parse_expression("a or (b and c)"))
self.assertEqual(len(expr), 2)
self.assertEqual(len(expr[0].genes), 1)
self.assertEqual(next(iter(expr[0].genes)).identifier, "a")
self.assertEqual(len(expr[1].genes), 2)
self.assertTrue(next(iter(expr[1].genes)).identifier, "b")
self.assertTrue(next(iter(expr[1].genes)).identifier, "c")
with self.assertRaises(InvalidGeneExpression):
gemtractor._parse_expression("a or a (b and c)")
with self.assertRaises(NotImplementedError):
pr = pp.ParseResults()
pr.append("a")
pr.append("and")
pr.append("b")
pr.append("or")
pr.append("c")
gemtractor._unfold_complex_expression(pr)
with self.assertRaises(NotImplementedError):
pr = pp.ParseResults()
pr.append("a")
pr.append("b")
gemtractor._unfold_complex_expression(pr)
def test_sbml(self):
f = "test/gene-filter-example.xml"
self.assertTrue(os.path.isfile(f), msg="cannot find test file")
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml()
self.assertEqual(sbml.getNumErrors(), 0)
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 3)
net.calc_genenet()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 3)
self.assertEqual(len(net.genes), 9)
self.assertEqual(len(net.gene_complexes), 3)
self.assertEqual(len(net.species["a"].occurence), 1)
self.assertEqual(len(net.species["b"].occurence), 2)
self.assertEqual(len(net.species["c"].occurence), 2)
self.assertEqual(len(net.reactions["r1"].consumed), 1)
self.assertEqual(len(net.reactions["r1"].produced), 1)
self.assertEqual(len(net.reactions["r1"].genes), 3)
self.assertEqual(len(net.reactions["r1"].genec), 3)
self.assertEqual(len(net.reactions["r2"].consumed), 1)
self.assertEqual(len(net.reactions["r2"].produced), 1)
self.assertEqual(len(net.reactions["r2"].genes), 2)
ns = net.serialize()
self.assertEqual(len(net.species), len(ns["species"]))
self.assertEqual(len(net.reactions), len(ns["reactions"]))
self.assertEqual(len(net.genes), len(ns["enzs"]))
self.assertEqual(len(net.gene_complexes), len(ns["enzc"]))
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 3)
links_in_rn = 0
for r in net.reactions:
links_in_rn += len(net.reactions[r].consumed) + len(
net.reactions[r].produced)
tf = tempfile.NamedTemporaryFile()
# test outputs
net.export_mn_dot(tf.name)
with open(tf.name, 'r') as r:
c = r.read().replace('\n', '')
self.assertEqual(c.count("label="),
len(ns["species"]) + len(ns["reactions"]))
self.assertEqual(c.count(" -> "), links_in_rn)
net.export_mn_gml(tf.name)
with open(tf.name, 'r') as r:
c = r.read().replace('\n', '')
self.assertEqual(c.count("node ["),
len(ns["species"]) + len(ns["reactions"]))
self.assertEqual(c.count("edge ["), links_in_rn)
net.export_mn_graphml(tf.name)
xmldoc = minidom.parse(tf.name)
self.assertEqual(len(xmldoc.getElementsByTagName('node')),
len(ns["species"]) + len(ns["reactions"]))
with open(tf.name, 'r') as r:
c = r.read().replace('\n', '')
self.assertEqual(c.count("<node "),
len(ns["species"]) + len(ns["reactions"]))
self.assertEqual(c.count(">species</data"), len(ns["species"]))
self.assertEqual(c.count(">reaction<"), len(ns["reactions"]))
self.assertEqual(c.count("<edge"), links_in_rn)
n_genelinks = 0
for g in net.genes:
n_genelinks += len(net.genes[g].links["g"])
n_genelinks += len(net.genes[g].links["gc"])
for g in net.gene_complexes:
n_genelinks += len(net.gene_complexes[g].links["g"])
n_genelinks += len(net.gene_complexes[g].links["gc"])
# test enzyme network
net.export_en_dot(tf.name)
with open(tf.name, 'r') as r:
c = r.read().replace('\n', '')
self.assertEqual(c.count("label="),
len(ns["enzs"]) + len(ns["enzc"]))
self.assertEqual(c.count(" -> "), n_genelinks)
net.export_en_gml(tf.name)
with open(tf.name, 'r') as r:
c = r.read().replace('\n', '')
self.assertEqual(c.count("node ["),
len(ns["enzs"]) + len(ns["enzc"]))
self.assertEqual(c.count("edge ["), n_genelinks)
net.export_en_graphml(tf.name)
xmldoc = minidom.parse(tf.name)
self.assertEqual(len(xmldoc.getElementsByTagName('node')),
len(ns["enzs"]) + len(ns["enzc"]))
with open(tf.name, 'r') as r:
c = r.read().replace('\n', '')
self.assertEqual(c.count("<node "),
len(ns["enzs"]) + len(ns["enzc"]))
self.assertEqual(c.count(">enzyme</data"), len(ns["enzs"]))
self.assertEqual(c.count(">enzyme_complex</data"), len(ns["enzc"]))
self.assertEqual(c.count("<edge"), n_genelinks)
net.export_en_sbml(tf.name, gemtractor, "testid")
gemtractor2 = GEMtractor(tf.name)
sbml = gemtractor2.get_sbml()
self.assertEqual(sbml.getNumErrors(), 0)
self.assertEqual(sbml.getModel().getNumSpecies(),
len(ns["enzs"]) + len(ns["enzc"]))
self.assertEqual(sbml.getModel().getNumReactions(), n_genelinks)
model = sbml.getModel()
found_x = False
for n in range(model.getNumSpecies()):
s = model.getSpecies(n)
identifier = s.getName()
if " + " in identifier:
# print (s.getAnnotationString ())
self.assertTrue("<bqbiol:hasPart>" in s.getAnnotationString())
self.assertEqual(
len(net.gene_complexes[identifier].genes),
s.getAnnotationString().count("<rdf:li rdf:resource="))
elif identifier == "x":
self.assertTrue(len(s.getAnnotationString()) > 100)
found_x = True
self.assertTrue(found_x, msg="didnt find gene x")
def test_sbml_filter2(self):
f = "test/gene-filter-example-2.xml"
self.assertTrue(os.path.isfile(f), msg="cannot find test file")
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml(filter_species=["a"], filter_genes=["a"])
self.assertEqual(sbml.getNumErrors(), 0)
self.assertTrue("modelid" in sbml.getModel().getName())
self.assertTrue("modelid" in sbml.getModel().getId())
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 3)
self.assertEqual(len(net.reactions["r1"].consumed), 0)
self.assertEqual(len(net.reactions["r1"].produced), 1)
self.assertEqual(len(net.reactions["r1"].genes), 2)
self.assertEqual(len(net.reactions["r1"].genec), 2)
self.assertEqual(len(net.reactions["r2"].consumed), 1)
self.assertEqual(len(net.reactions["r2"].produced), 1)
self.assertEqual(len(net.reactions["r1"].genes), 2)
self.assertEqual(len(net.reactions["r1"].genec), 2)
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml(filter_species=["b"],
remove_reaction_missing_species=False)
self.assertEqual(sbml.getNumErrors(), 0)
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 3)
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml(filter_species=["a", "b"])
self.assertEqual(sbml.getNumErrors(), 0)
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 2)
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml(filter_species=["a", "c"],
remove_reaction_missing_species=True)
self.assertEqual(sbml.getNumErrors(), 0)
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 2)
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml(filter_species=["a", "c"],
filter_reactions=["r3"],
remove_reaction_missing_species=True)
self.assertEqual(sbml.getNumErrors(), 0)
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 1)
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml(filter_genes=["x", "y"])
self.assertEqual(sbml.getNumErrors(), 0)
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 1)
gemtractor = GEMtractor(f)
sbml = gemtractor.get_sbml(filter_genes=["x", "y"],
remove_reaction_enzymes_removed=False)
self.assertEqual(sbml.getNumErrors(), 0)
net = gemtractor.extract_network_from_sbml()
self.assertEqual(len(net.species), 3)
self.assertEqual(len(net.reactions), 3)