def create_layout(n2lo, layout_model, layout_plugin, ub_sps, model):
h_min, (x_shift, y_shift), (w, h) = get_layout_characteristics(n2lo)
scale_factor = MARGIN * 1.0 / (h_min if h_min else 1)
(w, h) = scale((w, h), scale_factor)
(x_shift, y_shift) = shift(scale((x_shift, y_shift), scale_factor), MARGIN, MARGIN)
layout = layout_plugin.createLayout()
layout.setId(generate_unique_id(layout_model, "l_"))
l_id = layout.getId()
layout.setDimensions(create_dimensions(w + 2 * MARGIN, h + 2 * MARGIN))
for comp in model.getListOfCompartments():
c_id = comp.getId()
c_name = comp.getName()
if c_id in n2lo:
(x, y), (w, h) = n2lo[c_id]
(x, y), (w, h) = shift(scale((x, y), scale_factor), x_shift, y_shift), scale((w, h), scale_factor)
comp_glyph = layout.createCompartmentGlyph()
comp_glyph.setId("cg_%s_%s" % (l_id, c_id))
comp_glyph.setCompartmentId(c_id)
comp_glyph.setBoundingBox(create_bounding_box(x, y, w, h))
add_label(c_name, layout, comp_glyph, c_id, w, h, x, y)
for species in model.getListOfSpecies():
s_id = species.getId()
s_name = species.getName()
if s_id in n2lo:
if isinstance(n2lo[s_id], dict):
elements = n2lo[s_id].items()
else:
elements = [('', n2lo[s_id])]
for r_ids, [(x, y), (w, h)] in elements:
if not r_ids or next((it for it in (model.getReaction(r_id) for r_id in r_ids) if it), False):
(x, y), (w, h) = shift(scale((x, y), scale_factor), x_shift, y_shift), scale((w, h), scale_factor)
s_glyph = layout.createSpeciesGlyph()
s_glyph.setSpeciesId(s_id)
s_glyph_suffix = "%s_%s" % (s_id, '_'.join(r_ids)) if r_ids else s_id
s_glyph.setId("sg_%s_%s" % (l_id, s_glyph_suffix))
s_glyph.setBoundingBox(create_bounding_box(x, y, w, h))
add_label(s_name, layout, s_glyph, s_id, w, h, x, y)
for reaction in model.getListOfReactions():
r_id = reaction.getId()
r_name = reaction.getName()
if r_id in n2lo:
(x, y), (w, h) = n2lo[r_id]
(x, y), (w, h) = shift(scale((x, y), scale_factor), x_shift, y_shift), scale((w, h), scale_factor)
r_glyph = layout.createReactionGlyph()
r_glyph.setReactionId(r_id)
r_glyph.setId("rg_%s_%s" % (l_id, r_id))
r_glyph.setBoundingBox(create_bounding_box(x, y, w, h))
add_label(r_name, layout, r_glyph, r_id, w, h, x, y)
link_reaction_to_species(reaction.getListOfReactants(), r_glyph, l_id, r_id, n2lo,
lambda s_id: libsbml.SPECIES_ROLE_SIDESUBSTRATE
if s_id in ub_sps else libsbml.SPECIES_ROLE_SUBSTRATE)
link_reaction_to_species(reaction.getListOfProducts(), r_glyph, l_id, r_id, n2lo,
lambda s_id: libsbml.SPECIES_ROLE_SIDEPRODUCT
if s_id in ub_sps else libsbml.SPECIES_ROLE_PRODUCT)
def save_as_cytoscape_json(n2lo, model, out_json, ub_sp_ids):
"""
Converts a model with the given node and edge layout to a json file readable by Cytoscape.
:param ub_sp_ids: collection of ubiquitous species ids
:param n2lo: node layout as a dictionary {node_id: ((x, y), (w, h)) if node is not ubiquitous
else node_id : {r_ids: ((x, y), (w, h)) for r_ids of
reactions using each duplicated metabolite}}
:param model: SBML model
:param out_json: path where to save the resulting json file.
"""
# let's scale the map so that a minimal node has a width == 16 (so that the labels fit)
h_min, (x_shift, y_shift), _ = get_layout_characteristics(n2lo)
scale_factor = MARGIN * 1.0 / h_min if h_min else 1
(x_shift, y_shift) = shift(scale((x_shift, y_shift), scale_factor), MARGIN, MARGIN)
nodes, edges = [], []
for comp in model.getListOfCompartments():
c_id = comp.getId()
c_name = get_name(comp)
if c_id in n2lo:
(x, y), (w, h) = transform(n2lo[c_id], x_shift, y_shift, scale_factor)
nodes.append(get_node(x=x + w / 2, y=y + h / 2, z=-1,
**{NAME: c_name, ID: c_id, WEIGHT: w, HEIGHT: h, TYPE: TYPE_COMPARTMENT}))
for species in model.getListOfSpecies():
s_id = species.getId()
s_name = get_name(species)
glyph_type = UNSPECIFIED_ENTITY
sbo_term = species.getSBOTermID()
if sbo_term:
sbo_term = sbo_term.upper().strip()
if sbo_term in SBO_2_GLYPH_TYPE:
glyph_type = SBO_2_GLYPH_TYPE[sbo_term]
if s_id in n2lo:
if isinstance(n2lo[s_id], dict):
elements = n2lo[s_id].items()
else:
elements = [('', n2lo[s_id])]
for r_ids, coords in elements:
if not r_ids or next((it for it in (model.getReaction(r_id) for r_id in r_ids) if it), False):
(x, y), (w, h) = transform(coords, x_shift, y_shift, scale_factor)
nodes.append(
get_node(x=x + w / 2, y=y + h / 2, z=1,
**{GLYPH_TYPE: glyph_type, ID: "%s_%s" % (s_id, '_'.join(r_ids)) if r_ids else s_id,
COMPARTMENT: species.getCompartment(), NAME: s_name, WEIGHT: w, HEIGHT: h,
TYPE: TYPE_SPECIES, UBIQUITOUS: s_id in ub_sp_ids,
'ChEBI': get_chebi_id(species)}))
def get_sref_id(s_id):
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
return "%s_%s" % (s_id, '_'.join(r_ids))
return s_id
for reaction in model.getListOfReactions():
r_id = reaction.getId()
r_name = get_name(reaction)
ga = get_gene_association(reaction)
if r_id in n2lo:
(x, y), (w, h) = transform(n2lo[r_id], x_shift, y_shift, scale_factor)
nodes.append(get_node(x=x + w / 2, y=y + h / 2, z=1,
**{ID: r_id, NAME: ga, WEIGHT: w, HEIGHT: h, TYPE: TYPE_REACTION,
REVERSIBLE: reaction.getReversible(),
UBIQUITOUS:
next((False for s_id in chain(get_reactants(reaction), get_products(reaction))
if s_id not in ub_sp_ids), True),
'genes': ga, 'r_name': r_name}))
for s_id in get_reactants(reaction):
edges.append(get_edge(**{ID: "%s_%s" % (r_id, s_id), SOURCE: r_id, TARGET: get_sref_id(s_id),
NAME: '%s is a substrate of %s' % (get_name(model.getSpecies(s_id)), r_name),
UBIQUITOUS: s_id in ub_sp_ids, INTERACTION: SUBSTRATE}))
for s_id in get_products(reaction):
edges.append(get_edge(**{ID: "%s_%s" % (r_id, s_id), SOURCE: r_id, TARGET: get_sref_id(s_id),
NAME: '%s is a product of %s' % (get_name(model.getSpecies(s_id)), r_name),
UBIQUITOUS: s_id in ub_sp_ids, INTERACTION: PRODUCT}))
save_cyjson(nodes, edges, out_json)
def process_sbml(sbml,
verbose,
ub_ch_ids=None,
web_page_prefix=None,
generalize=True,
log_file=None,
id2mask=None,
layer2mask=DEFAULT_LAYER2MASK,
tab2html=None,
title=None,
h1=None,
id2color=None,
tabs={ABOUT_TAB, DOWNLOAD_TAB},
info='',
invisible_layers=None,
sbgn=True,
cytoscape=True):
"""
Generalizes and visualizes a given SBML model.
:param sbml: a path to the input SBML file
:param verbose: if logging information should be printed
:param ub_ch_ids: optional, ChEBI ids to be considered as ubiquitous. If left None, will be calculated automatically.
:param web_page_prefix: optional, how this model's webpage will be identified.
If left None an identifier will be generated based on the SBML file's md5.
:param generalize: optional, whether the generalization should be performed. The default is True
:param log_file: optional, a file where the logging information should be redirected
(only needed if verbose is set to True)
:param id2mask: optional,
:param layer2mask: optional, a dict storing the correspondence between a layer name and an its id mask
:param tab2html: optional,
:param title: optional, the title for the web page
:param h1: optional, the main header of the web page
:param id2color: optional,
:param tabs: optional, a set of names of tabs that should be shown
:param info: optional, additional information to be displayed in the bottom of the web page
:param invisible_layers: optional, the layers of the visualized metabolic map that should be hidden
:return: void
"""
# Read the SBML
reader = libsbml.SBMLReader()
doc = reader.readSBML(sbml)
model = doc.getModel()
if not model:
raise Exception(
"The model should be in SBML format, check your file %s" % sbml)
model_id = model.getId()
if not model_id:
sbml_name = os.path.splitext(os.path.basename(sbml))[0]
model.setId(sbml_name)
model_id = sbml_name
# Prepare the output directories
web_page_prefix = web_page_prefix if web_page_prefix else check_md5(sbml)
sbml_dir = dirname(abspath(sbml))
directory = os.path.join(sbml_dir, web_page_prefix)
if not os.path.exists(directory):
os.makedirs(directory)
lib_path = os.path.join(directory, 'lib')
if not os.path.exists(lib_path):
copytree(get_lib(), lib_path)
# Prepare the logger
if verbose:
logging.captureWarnings(True)
logging.basicConfig(level=logging.INFO,
format='%(asctime)s: %(message)s',
datefmt="%Y-%m-%d %H:%M:%S",
filename=log_file)
# Generalize the model if needed
groups_sbml = os.path.join(directory, '%s_with_groups.xml' % model_id)
gen_sbml = os.path.join(directory, '%s_generalized.xml' % model_id)
if check_for_groups(sbml, SBO_CHEMICAL_MACROMOLECULE,
GROUP_TYPE_UBIQUITOUS):
if sbml != groups_sbml:
if not libsbml.SBMLWriter().writeSBMLToFile(doc, groups_sbml):
raise Exception("Could not write your model to %s" %
groups_sbml)
else:
chebi = parse_simple(get_chebi())
if generalize:
logging.info('Generalizing the model...')
generalize_model(sbml,
chebi,
groups_sbml,
gen_sbml,
ub_chebi_ids=ub_ch_ids)
else:
gen_sbml = None
logging.info('Ubiquitizing the model...')
ubiquitize_model(sbml, chebi, groups_sbml, ub_chebi_ids=ub_ch_ids)
# Visualize the model
reader = libsbml.SBMLReader()
input_document = reader.readSBML(groups_sbml)
input_model = input_document.getModel()
root, c_id2info, c_id2outs, chebi, ub_sps = import_sbml(
input_model, groups_sbml)
c_id2out_c_id = {}
for c_id, c_info in c_id2info.items():
_, _, (_, out_c_id) = c_info
if out_c_id:
c_id2out_c_id[c_id] = out_c_id
try:
n2xy = parse_layout_sbml(sbml)
if n2xy:
logging.info('Found layout in the model...')
r_size = next((n2xy[r.getId()][1][0]
for r in input_model.getListOfReactions()
if r.getId() in n2xy), None)
if r_size:
scale_factor = REACTION_SIZE / r_size
if scale_factor != 1:
keys = n2xy.keys()
for n_id in keys:
value = n2xy[n_id]
if isinstance(value, dict):
value = {
r_id:
(scale(xy,
scale_factor), scale(wh, scale_factor))
for (r_id, (xy, wh)) in value.items()
}
else:
xy, wh = value
value = scale(xy, scale_factor), scale(
wh, scale_factor)
n2xy[n_id] = value
except LoPlError:
n2xy = None
fc, (n2lo, e2lo), hidden_c_ids, c_id_hidden_ubs = \
graph2geojson(c_id2info, c_id2outs, root, n2xy, id2mask=id2mask, onto=chebi,
colorer=color if not id2color else lambda graph: color_by_id(graph, id2color))
if n2lo:
groups_document = reader.readSBML(groups_sbml)
groups_model = groups_document.getModel()
if gen_sbml:
gen_document = reader.readSBML(gen_sbml)
gen_model = gen_document.getModel()
else:
gen_model = False
save_as_layout_sbml(groups_model, gen_model, groups_sbml, gen_sbml,
n2lo, ub_sps)
if sbgn:
groups_sbgn = os.path.join(directory, '%s.sbgn' % model_id)
gen_sbgn = os.path.join(directory,
'%s_generalized.sbgn' % model_id)
try:
save_as_sbgn(n2lo, e2lo, groups_model, groups_sbgn)
logging.info(' exported as SBGN %s' % groups_sbgn)
except Exception as e:
logging.error("Didn't manage to save to SBGN: %s" % e)
if gen_model:
try:
save_as_sbgn(n2lo, e2lo, gen_model, gen_sbgn)
logging.info(' exported as SBGN %s' % groups_sbgn)
except Exception as e:
logging.error("Didn't manage to save to SBGN: %s" % e)
if cytoscape:
out_json = os.path.join(directory, '%s.cyjs' % model_id)
save_as_cytoscape_json(n2lo, model, out_json, ub_sps)
logging.info(' exported as Cytoscape json %s' % out_json)
if gen_model:
out_json = os.path.join(directory,
'%s_generalized.cyjs' % model_id)
save_as_cytoscape_json(n2lo, gen_model, out_json, ub_sps)
# Serialize the result
serialize(directory=directory,
m_dir_id=web_page_prefix,
input_model=input_model,
c_id2level2features=fc,
c_id2out_c_id=c_id2out_c_id,
hidden_c_ids=hidden_c_ids,
c_id_hidden_ubs=c_id_hidden_ubs,
tabs=tabs,
groups_sbml=groups_sbml,
layer2mask=layer2mask,
tab2html=tab2html,
title=title,
h1=h1,
invisible_layers=invisible_layers)
def save_as_sbgn(n2lo, e2lo, model, out_sbgn):
"""
Converts a model with the given node and edge layout to SBGN PD (see http://www.sbgn.org/).
:param n2lo: node layout as a dictionary {node_id: ((x, y), (w, h)) if node is not ubiquitous
else node_id : {r_ids: ((x, y), (w, h)) for r_ids of
reactions using each duplicated metabolite}}
:param e2lo: edge layout as a dictionary {edge_id: [(x_start, y_start), (x_bend_0, y_bend_0),..,(x_end, y_end)]},
where edge_id = "-".join(sorted((metabolite_id, reaction_id))).
:param model: SBML model
:param out_sbgn: path where to save the resulting SBGN file.
"""
# let's scale the map so that a minimal node has a width == 16 (so that the labels fit)
h_min, (x_shift, y_shift), (w, h) = get_layout_characteristics(n2lo)
scale_factor = MARGIN * 1.0 / h_min if h_min else 1
(w, h) = scale((w, h), scale_factor)
(x_shift, y_shift) = shift(scale((x_shift, y_shift), scale_factor), MARGIN, MARGIN)
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
sbgn_map = libsbgn.map()
sbgn_map.set_language(Language.PD)
sbgn.set_map(sbgn_map)
# create a bounding box for the map
box = libsbgn.bbox(0, 0, w + 2 * MARGIN, h + 2 * MARGIN)
sbgn_map.set_bbox(box)
# glyphs with labels
for comp in model.getListOfCompartments():
c_id = comp.getId()
c_name = comp.getName()
if not c_name:
c_name = c_id
if c_id in n2lo:
(x, y), (w, h) = transform(n2lo[c_id], x_shift, y_shift, scale_factor)
g = libsbgn.glyph(class_=GlyphClass.COMPARTMENT, id=c_id)
g.set_label(libsbgn.label(text=c_name, bbox=libsbgn.bbox(x, y, w, h)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
for species in model.getListOfSpecies():
s_id = species.getId()
s_name = species.getName()
glyph_type = GlyphClass.UNSPECIFIED_ENTITY
sbo_term = species.getSBOTermID()
if sbo_term:
sbo_term = sbo_term.upper().strip()
if sbo_term in SBO_2_GLYPH_TYPE:
glyph_type = SBO_2_GLYPH_TYPE[sbo_term]
if not s_name:
s_name = s_id
if s_id in n2lo:
if isinstance(n2lo[s_id], dict):
elements = n2lo[s_id].items()
else:
elements = [('', n2lo[s_id])]
for r_ids, coords in elements:
if not r_ids or next((it for it in (model.getReaction(r_id) for r_id in r_ids) if it), False):
(x, y), (w, h) = transform(coords, x_shift, y_shift, scale_factor)
g = libsbgn.glyph(class_=glyph_type, id="%s_%s" % (s_id, '_'.join(r_ids)) if r_ids else s_id,
compartmentRef=species.getCompartment())
g.set_label(libsbgn.label(text=s_name,
bbox=libsbgn.bbox(x + w * 0.1, y + h * 0.1, w * 0.8, h * 0.8)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
# glyph with ports (process)
for reaction in model.getListOfReactions():
r_id = reaction.getId()
if r_id in n2lo:
(x, y), (w, h) = transform(n2lo[r_id], x_shift, y_shift, scale_factor)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id=r_id)
g.set_bbox(libsbgn.bbox(x, y, w, h))
rev = reaction.getReversible()
in_port = None
for s_id in (species_ref.getSpecies() for species_ref in reaction.getListOfReactants()):
edge_id = "-".join(sorted((s_id, r_id)))
if edge_id in e2lo:
xy_list = e2lo[edge_id]
if not in_port:
port_x, port_y = shift(scale(xy_list[-2] if len(xy_list) > 2 else xy_list[-1], scale_factor),
x_shift, y_shift)
in_port = libsbgn.port(x=port_x, y=port_y, id="%s__in" % r_id)
g.add_port(in_port)
sref_id = s_id
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
sref_id = "%s_%s" % (s_id, '_'.join(r_ids))
a = libsbgn.arc(class_=ArcClass.PRODUCTION if rev else ArcClass.CONSUMPTION,
target=sref_id if rev else in_port.get_id(),
source=in_port.get_id() if rev else sref_id, id="a_%s_%s" % (s_id, r_id))
s_x, s_y = shift(scale(xy_list[0], scale_factor), x_shift, y_shift)
a.set_start(libsbgn.startType(x=in_port.get_x() if rev else s_x, y=in_port.get_y() if rev else s_y))
a.set_end(libsbgn.endType(x=s_x if rev else in_port.get_x(), y=s_y if rev else in_port.get_y()))
sbgn_map.add_arc(a)
out_port = None
for s_id in (species_ref.getSpecies() for species_ref in reaction.getListOfProducts()):
edge_id = "-".join(sorted((s_id, r_id)))
if edge_id in e2lo:
xy_list = e2lo[edge_id]
if not out_port:
port_x, port_y = shift(scale(xy_list[1] if len(xy_list) > 2 else xy_list[0], scale_factor),
x_shift, y_shift)
out_port = libsbgn.port(x=port_x, y=port_y, id="%s__out" % r_id)
g.add_port(out_port)
sref_id = s_id
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
sref_id = "%s_%s" % (s_id, '_'.join(r_ids))
a = libsbgn.arc(class_=ArcClass.PRODUCTION, target=sref_id, source=out_port.get_id(),
id="a_%s_%s" % (r_id, s_id))
s_x, s_y = shift(scale(xy_list[-1], scale_factor), x_shift, y_shift)
a.set_end(libsbgn.startType(x=s_x, y=s_y))
a.set_start(libsbgn.endType(x=out_port.get_x(), y=out_port.get_y()))
sbgn_map.add_arc(a)
sbgn_map.add_glyph(g)
# write everything to a file
sbgn.write_file(out_sbgn)
def save_as_sbgn(n2lo, e2lo, model, out_sbgn):
"""
Converts a model with the given node and edge layout to SBGN PD (see http://www.sbgn.org/).
:param n2lo: node layout as a dictionary {node_id: ((x, y), (w, h)) if node is not ubiquitous
else node_id : {r_ids: ((x, y), (w, h)) for r_ids of
reactions using each duplicated metabolite}}
:param e2lo: edge layout as a dictionary {edge_id: [(x_start, y_start), (x_bend_0, y_bend_0),..,(x_end, y_end)]},
where edge_id = "-".join(sorted((metabolite_id, reaction_id))).
:param model: SBML model
:param out_sbgn: path where to save the resulting SBGN file.
"""
# let's scale the map so that a minimal node has a width == 16 (so that the labels fit)
h_min, (x_shift, y_shift), (w, h) = get_layout_characteristics(n2lo)
scale_factor = MARGIN * 1.0 / h_min if h_min else 1
(w, h) = scale((w, h), scale_factor)
(x_shift, y_shift) = shift(scale((x_shift, y_shift), scale_factor), MARGIN,
MARGIN)
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
sbgn_map = libsbgn.map()
sbgn_map.set_language(Language.PD)
sbgn.set_map(sbgn_map)
# create a bounding box for the map
box = libsbgn.bbox(0, 0, w + 2 * MARGIN, h + 2 * MARGIN)
sbgn_map.set_bbox(box)
# glyphs with labels
for comp in model.getListOfCompartments():
c_id = comp.getId()
c_name = comp.getName()
if not c_name:
c_name = c_id
if c_id in n2lo:
(x, y), (w, h) = transform(n2lo[c_id], x_shift, y_shift,
scale_factor)
g = libsbgn.glyph(class_=GlyphClass.COMPARTMENT, id=c_id)
g.set_label(
libsbgn.label(text=c_name, bbox=libsbgn.bbox(x, y, w, h)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
for species in model.getListOfSpecies():
s_id = species.getId()
s_name = species.getName()
glyph_type = GlyphClass.UNSPECIFIED_ENTITY
sbo_term = species.getSBOTermID()
if sbo_term:
sbo_term = sbo_term.upper().strip()
if sbo_term in SBO_2_GLYPH_TYPE:
glyph_type = SBO_2_GLYPH_TYPE[sbo_term]
if not s_name:
s_name = s_id
if s_id in n2lo:
if isinstance(n2lo[s_id], dict):
elements = n2lo[s_id].items()
else:
elements = [('', n2lo[s_id])]
for r_ids, coords in elements:
if not r_ids or next(
(it for it in (model.getReaction(r_id)
for r_id in r_ids) if it), False):
(x, y), (w, h) = transform(coords, x_shift, y_shift,
scale_factor)
g = libsbgn.glyph(
class_=glyph_type,
id="%s_%s" %
(s_id, '_'.join(r_ids)) if r_ids else s_id,
compartmentRef=species.getCompartment())
g.set_label(
libsbgn.label(text=s_name,
bbox=libsbgn.bbox(
x + w * 0.1, y + h * 0.1, w * 0.8,
h * 0.8)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
# glyph with ports (process)
for reaction in model.getListOfReactions():
r_id = reaction.getId()
if r_id in n2lo:
(x, y), (w, h) = transform(n2lo[r_id], x_shift, y_shift,
scale_factor)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id=r_id)
g.set_bbox(libsbgn.bbox(x, y, w, h))
rev = reaction.getReversible()
in_port = None
for s_id in (species_ref.getSpecies()
for species_ref in reaction.getListOfReactants()):
edge_id = "-".join(sorted((s_id, r_id)))
if edge_id in e2lo:
xy_list = e2lo[edge_id]
if not in_port:
port_x, port_y = shift(
scale(
xy_list[-2] if len(xy_list) > 2 else
xy_list[-1], scale_factor), x_shift, y_shift)
in_port = libsbgn.port(x=port_x,
y=port_y,
id="%s__in" % r_id)
g.add_port(in_port)
sref_id = s_id
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
sref_id = "%s_%s" % (s_id, '_'.join(r_ids))
a = libsbgn.arc(
class_=ArcClass.PRODUCTION
if rev else ArcClass.CONSUMPTION,
target=sref_id if rev else in_port.get_id(),
source=in_port.get_id() if rev else sref_id,
id="a_%s_%s" % (s_id, r_id))
s_x, s_y = shift(scale(xy_list[0], scale_factor), x_shift,
y_shift)
a.set_start(
libsbgn.startType(x=in_port.get_x() if rev else s_x,
y=in_port.get_y() if rev else s_y))
a.set_end(
libsbgn.endType(x=s_x if rev else in_port.get_x(),
y=s_y if rev else in_port.get_y()))
sbgn_map.add_arc(a)
out_port = None
for s_id in (species_ref.getSpecies()
for species_ref in reaction.getListOfProducts()):
edge_id = "-".join(sorted((s_id, r_id)))
if edge_id in e2lo:
xy_list = e2lo[edge_id]
if not out_port:
port_x, port_y = shift(
scale(
xy_list[1] if len(xy_list) > 2 else xy_list[0],
scale_factor), x_shift, y_shift)
out_port = libsbgn.port(x=port_x,
y=port_y,
id="%s__out" % r_id)
g.add_port(out_port)
sref_id = s_id
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
sref_id = "%s_%s" % (s_id, '_'.join(r_ids))
a = libsbgn.arc(class_=ArcClass.PRODUCTION,
target=sref_id,
source=out_port.get_id(),
id="a_%s_%s" % (r_id, s_id))
s_x, s_y = shift(scale(xy_list[-1], scale_factor), x_shift,
y_shift)
a.set_end(libsbgn.startType(x=s_x, y=s_y))
a.set_start(
libsbgn.endType(x=out_port.get_x(),
y=out_port.get_y()))
sbgn_map.add_arc(a)
sbgn_map.add_glyph(g)
# write everything to a file
sbgn.write_file(out_sbgn)
