def test_bound_condition():
bc = BoundCondition(Agent('RAF1'), True)
st = Phosphorylation(Agent('BRAF', bound_conditions=[bc]), Agent('MAP2K1'))
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def test_activeform():
erkact = Agent('MAPK1', activity=ActivityCondition('kinase', True))
erkelk = Phosphorylation(erkact, Agent('ELK1'))
erkp = Agent('MAPK1', mods=[ModCondition('phosphorylation')])
st = ActiveForm(erkp, 'kinase', True)
sa = SBGNAssembler([st, erkelk])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def test_complex():
egfr1 = Agent('EGFR',
bound_conditions=[BoundCondition(Agent('EGF'), True)])
egfr2 = Agent('EGFR',
bound_conditions=[BoundCondition(Agent('EGF'), True)])
st = Complex([egfr1, egfr2])
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def _make_sbgn(stmts):
sa = SBGNAssembler()
sa.add_statements(stmts)
sa.make_model()
sbgn_str = sa.print_model()
logger.info(sbgn_str)
return sbgn_str
def _make_sbgn(stmts):
sa = SBGNAssembler()
sa.add_statements(stmts)
sa.make_model()
sbgn_str = sa.print_model()
logger.info(sbgn_str)
return sbgn_str
def export_sbgn(model):
"""Return an SBGN model string corresponding to the PySB model.
This function first calls generate_equations on the PySB model to obtain
a reaction network (i.e. individual species, reactions). It then iterates
over each reaction and and instantiates its reactants, products, and the
process itself as SBGN glyphs and arcs.
Parameters
----------
model : pysb.core.Model
A PySB model to be exported into SBGN
Returns
-------
sbgn_str : str
An SBGN model as string
"""
import lxml.etree
import lxml.builder
from pysb.bng import generate_equations
from indra.assemblers.sbgn import SBGNAssembler
logger.info('Generating reaction network with BNG for SBGN export. ' +
'This could take a long time.')
generate_equations(model)
sa = SBGNAssembler()
glyphs = {}
for idx, species in enumerate(model.species):
glyph = sa._glyph_for_complex_pattern(species)
if glyph is None:
continue
sa._map.append(glyph)
glyphs[idx] = glyph
for reaction in model.reactions:
# Get all the reactions / products / controllers of the reaction
reactants = set(reaction['reactants']) - set(reaction['products'])
products = set(reaction['products']) - set(reaction['reactants'])
controllers = set(reaction['reactants']) & set(reaction['products'])
# Add glyph for reaction
process_glyph = sa._process_glyph('process')
# Connect reactants with arcs
if not reactants:
glyph_id = sa._none_glyph()
sa._arc('consumption', glyph_id, process_glyph)
else:
for r in reactants:
glyph = glyphs.get(r)
if glyph is None:
glyph_id = sa._none_glyph()
else:
glyph_id = glyph.attrib['id']
sa._arc('consumption', glyph_id, process_glyph)
# Connect products with arcs
if not products:
glyph_id = sa._none_glyph()
sa._arc('production', process_glyph, glyph_id)
else:
for p in products:
glyph = glyphs.get(p)
if glyph is None:
glyph_id = sa._none_glyph()
else:
glyph_id = glyph.attrib['id']
sa._arc('production', process_glyph, glyph_id)
# Connect controllers with arcs
for c in controllers:
glyph = glyphs[c]
sa._arc('catalysis', glyph.attrib['id'], process_glyph)
sbgn_str = sa.print_model().decode('utf-8')
return sbgn_str
def test_increaseamount():
st = IncreaseAmount(Agent(''), Agent('MAP2K1'))
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 3, 2)
def test_inhibition():
st = Inhibition(Agent('BRAF'), Agent('MAP2K1'))
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def test_remove_modification():
st = Deacetylation(Agent('BRAF'), Agent('MAP2K1'))
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def assemble_sbgn(model_name, statements):
# SBGN assembly
sa = SBGNAssembler()
sa.add_statements(statements)
sa.make_model()
sa.save_model('%s_sbgn.xml' % model_name)
def assemble_sbgn(model_name, statements):
# SBGN assembly
sa = SBGNAssembler()
sa.add_statements(statements)
sa.make_model()
sa.save_model('%s_sbgn.xml' % model_name)
def export_sbgn(model):
"""Return an SBGN model string corresponding to the PySB model.
This function first calls generate_equations on the PySB model to obtain
a reaction network (i.e. individual species, reactions). It then iterates
over each reaction and and instantiates its reactants, products, and the
process itself as SBGN glyphs and arcs.
Parameters
----------
model : pysb.core.Model
A PySB model to be exported into SBGN
Returns
-------
sbgn_str : str
An SBGN model as string
"""
import lxml.etree
import lxml.builder
from pysb.bng import generate_equations
from indra.assemblers.sbgn import SBGNAssembler
logger.info('Generating reaction network with BNG for SBGN export. ' +
'This could take a long time.')
generate_equations(model)
sa = SBGNAssembler()
glyphs = {}
for idx, species in enumerate(model.species):
glyph = sa._glyph_for_complex_pattern(species)
if glyph is None:
continue
sa._map.append(glyph)
glyphs[idx] = glyph
for reaction in model.reactions:
# Get all the reactions / products / controllers of the reaction
reactants = set(reaction['reactants']) - set(reaction['products'])
products = set(reaction['products']) - set(reaction['reactants'])
controllers = set(reaction['reactants']) & set(reaction['products'])
# Add glyph for reaction
process_glyph = sa._process_glyph('process')
# Connect reactants with arcs
if not reactants:
glyph_id = sa._none_glyph()
sa._arc('consumption', glyph_id, process_glyph)
else:
for r in reactants:
glyph = glyphs.get(r)
if glyph is None:
glyph_id = sa._none_glyph()
else:
glyph_id = glyph.attrib['id']
sa._arc('consumption', glyph_id, process_glyph)
# Connect products with arcs
if not products:
glyph_id = sa._none_glyph()
sa._arc('production', process_glyph, glyph_id)
else:
for p in products:
glyph = glyphs.get(p)
if glyph is None:
glyph_id = sa._none_glyph()
else:
glyph_id = glyph.attrib['id']
sa._arc('production', process_glyph, glyph_id)
# Connect controllers with arcs
for c in controllers:
glyph = glyphs[c]
sa._arc('catalysis', glyph.attrib['id'], process_glyph)
sbgn_str = sa.print_model().decode('utf-8')
return sbgn_str