def write_sbgn_01(f):
"""Create SBGN and write to file.
Macromolecule box with label.
:param f: file to write to
:return:
"""
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a glyph with an id and class "macromolecule"
g1 = libsbgn.glyph()
g1.set_id("glyph1")
g1.set_class(GlyphClass.MACROMOLECULE)
# add the glyph to the map
map.add_glyph(g1)
# define the bounding box of the glyph
bbox1 = libsbgn.bbox(x=125, y=60, w=100, h=40)
g1.set_bbox(bbox1)
# define a label for this glyph
label1 = libsbgn.label()
label1.set_text("P53")
# now write everything to disk
sbgn.write_file(f)
def write_glyph_notes(f):
""" Set notes on element.
:return:
"""
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a glyph with an id and class "macromolecule"
g = libsbgn.glyph()
g.set_id("g1")
# define a label for this glyph
label = libsbgn.label()
label.set_text("INSR")
bbox = libsbgn.bbox(x=100, y=100, w=80, h=40)
g.set_bbox(bbox)
map.add_glyph(g)
notes = Notes("""
<body xmlns="http://www.w3.org/1999/xhtml">
This is an example note describing the INSR glyph.
</body>""")
g.set_notes(notes)
print(utils.write_to_string(sbgn))
utils.write_to_file(sbgn=sbgn, f=f)
def test_read_notes():
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
text = """
<body xmlns="http://www.w3.org/1999/xhtml">
This is an example note describing the map.
</body>
"""
notes = Notes(text)
map.set_notes(notes)
assert map.get_notes() is not None
f = tempfile.NamedTemporaryFile(suffix=".sbgn")
utils.write_to_file(sbgn, f.name)
del map, sbgn, notes
sbgn2 = utils.read_from_file(f.name)
print(utils.write_to_string(sbgn2))
map2 = sbgn2.get_map()
notes2 = map2.get_notes()
assert notes2 is not None
assert "<body" in str(notes2)
def test_read_extension():
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
extension = Extension(
"""<renderInformation id="example" programName="SBML Layout" programVersion="3.0"
xmlns="http://projects.eml.org/bcb/sbml/render/level2">
<listOfColorDefinitions>
<colorDefinition id="yelloComp" value="#ffffccff" />
<colorDefinition id="grayComp" value="#e0e0e0ff" />
<colorDefinition id="orange" value="#fa9e2fff" />
<colorDefinition id="blue" value="#2958acff" />
<colorDefinition id="green" value="#378f5cff" />
<colorDefinition id="Color_0" value="#969696" />
<colorDefinition id="Color_1" value="#ff9900" />
<colorDefinition id="Color_2" value="#000000" />
</listOfColorDefinitions>
</renderInformation>"""
)
map.set_extension(extension)
assert map.get_extension() is not None
f = tempfile.NamedTemporaryFile(suffix=".sbgn")
utils.write_to_file(sbgn, f.name)
del map, sbgn, extension
sbgn = utils.read_from_file(f.name)
map = sbgn.get_map()
extension = map.get_extension()
assert extension is not None
assert "<colorDefinition" in str(extension)
def write_glyph_notes(f):
"""Set notes on element.
:return: None
"""
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a glyph with an id and class "macromolecule"
g = libsbgn.glyph()
g.set_id("g1")
# define a label for this glyph
label = libsbgn.label()
label.set_text("INSR")
bbox = libsbgn.bbox(x=100, y=100, w=80, h=40)
g.set_bbox(bbox)
map.add_glyph(g)
notes = Notes("""
<body xmlns="http://www.w3.org/1999/xhtml">
This is an example note describing the INSR glyph.
</body>""")
g.set_notes(notes)
print(utils.write_to_string(sbgn))
utils.write_to_file(sbgn=sbgn, f=f)
def write_sbgn_01(f):
""" Create SBGN and write to file.
Macromolecule box with label.
:param f: file to write to
:return:
"""
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a glyph with an id and class "macromolecule"
g1 = libsbgn.glyph()
g1.set_id("glyph1")
g1.set_class(GlyphClass.MACROMOLECULE)
# add the glyph to the map
map.add_glyph(g1)
# define the bounding box of the glyph
bbox1 = libsbgn.bbox(x=125, y=60, w=100, h=40)
g1.set_bbox(bbox1)
# define a label for this glyph
label1 = libsbgn.label()
label1.set_text("P53")
# now write everything to disk
sbgn.write_file(f)
def test_create_notes():
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a glyph with an id and class "macromolecule"
g = libsbgn.glyph()
g.set_id("g1")
# define a label for this glyph
label = libsbgn.label()
label.set_text("INSR")
bbox = libsbgn.bbox(x=100, y=100, w=80, h=40)
g.set_bbox(bbox)
map.add_glyph(g)
notes = Notes(
"""
<body xmlns="http://www.w3.org/1999/xhtml">
This is an example note describing the INSR glyph.
</body>"""
)
g.set_notes(notes)
assert g.get_notes() is not None
notes_str = str(g.get_notes())
assert "<body" in notes_str
def __init__(self, fichier_entree, fichier_sortie):
self.data = codecs.open(fichier_entree, 'r', 'utf8')
self.sbgn = libsbgn.sbgn()
self.map = libsbgn.map()
self.map.set_language(Language.AF)
self.sbgn.set_map(self.map)
self.f_out = fichier_sortie
#résolution de l'image : pixels / inch
self.resolution = ParamsLogToAF.RESOLUTION
#compteur de glyphs
self.nb_glyph = 0
#compteur d'arcs
self.nb_arc = 0
#dictionnaire qui fait correspondre les constantes logiques
#associées aux glyphes (clé) avec les glyphs eux-mêmes.
self.dic_const_glyph = {}
#dictionnaire qui relie les glyphs (clés) aux arcs auxquels ils
#participent en tant que source ou target, stockés sous forme
#de liste de tuples : ('s' ou 't', arc).
self.dic_glyph_arc = {}
#dictionnaire qui permet d'accéder aux glyphs à partir de leur
#id (clé)
self.dic_id_glyph = {}
#dictionnaire qui permet d'accéder aux glyphs contenus dans
#un compartment (clé)
self.dic_comp = {}
#liste des glyphs n'appartenant à aucun compartment
#initialisée quand tous les glyphs sont créés
self.single_glyph = []
#dictionnaire de fonctions:
#associe un predicat à la fonction correpondante.
self.dic_func = {'compartment' : self.create_glyph,
'ba' : self.create_glyph, 'perturbation' : self.create_glyph,
'phenotype' : self.create_glyph, 'and' : self.create_glyph,
'or' : self.create_glyph, 'not' : self.create_glyph,
'delay' : self.create_glyph, 'label' : self.create_label,
'input' : self.create_arc, 'stimulates' : self.create_arc,
'inhibits' : self.create_arc,
'unknownInfluences' : self.create_arc,
'necessarilyStimulates' : self.create_arc,
'localized' : self.create_localisation,
'uoi' : self.create_unitOfInformation,
'biologicalActivity' : self.create_glyph}
#Graphe en langage DOT
self.dot_graph = Digraph('G', filename='position_graph_sbgn.gv',
format='plain', encoding='utf8')
#hauteur et largeur du graphe en pixels : mise à jour au moment
#de la lecture du fichier .gv.plain
self.max_height = 0
self.max_width = 0
def write_sbgn_03(f):
"""Create SBGN with annotation and write to file.
:param f: file to write
:return:
"""
from libsbgnpy.libsbgn import bbox, calloutType, glyph, label, map, point, sbgn
doc = sbgn()
m = map()
m.set_language(Language.PD)
doc.set_map(m)
# create a glyph with an id and class "macromolecule"
g1 = glyph()
g1.set_id("g1")
g1.set_class(GlyphClass.MACROMOLECULE)
# create a glyph with an id and class "annotation"
g2 = glyph()
g2.set_id("g2")
g2.set_class(GlyphClass.ANNOTATION)
co = calloutType()
co.set_target(g1)
p = point(x=160, y=200)
co.set_point(p)
g2.set_callout(co)
# add the glyph to the map
m.add_glyph(g1)
m.add_glyph(g2)
# define the bounding box of the glyph
bbox1 = bbox(x=90, y=160, w=380, h=210)
g1.set_bbox(bbox1)
# define the bounding box of the annotation
bbox2 = bbox(x=5, y=5, w=220, h=125)
g2.set_bbox(bbox2)
# define a label for this glyph
label1 = label(text="LABEL")
g1.set_label(label1)
# define a label for this annotation
label2 = label(text="INFO")
g2.set_label(label2)
# now write everything to disk
doc.write_file(f)
def write_sbgn_03(f):
""" Create SBGN with annotation and write to file.
:param f: file to write
:return:
"""
from libsbgnpy.libsbgn import sbgn, map, glyph, point, calloutType, bbox, label
doc = sbgn()
m = map()
m.set_language(Language.PD)
doc.set_map(m)
# create a glyph with an id and class "macromolecule"
g1 = glyph()
g1.set_id("g1")
g1.set_class(GlyphClass.MACROMOLECULE)
# create a glyph with an id and class "annotation"
g2 = glyph()
g2.set_id("g2")
g2.set_class(GlyphClass.ANNOTATION)
co = calloutType()
co.set_target(g1)
p = point(x=160, y=200)
co.set_point(p)
g2.set_callout(co)
# add the glyph to the map
m.add_glyph(g1)
m.add_glyph(g2)
# define the bounding box of the glyph
bbox1 = bbox(x=90, y=160, w=380, h=210)
g1.set_bbox(bbox1)
# define the bounding box of the annotation
bbox2 = bbox(x=5, y=5, w=220, h=125)
g2.set_bbox(bbox2)
# define a label for this glyph
label1 = label(text="LABEL")
g1.set_label(label1)
# define a label for this annotation
label2 = label(text="INFO")
g2.set_label(label2)
# now write everything to disk
doc.write_file(f)
def write(net, filename, renew_ids=False):
"""Writes a map to an SBGN-ML file
:param filename: the SBGN-ML file to be created
:param renew_ids: if True, renews the ids of the glyphs
"""
sbgn = libsbgn.sbgn()
sbgnmap = libsbgn.map()
language = libsbgn.Language.PD
sbgnmap.set_language(language)
sbgn.set_map(sbgnmap)
dids = {}
if renew_ids:
net.renew_ids()
for comp in net.compartments:
g = _make_glyph_from_compartment(comp)
sbgnmap.add_glyph(g)
dids[str(comp)] = g.get_id()
for entity in net.entities:
g = _make_glyph_from_entity(entity, dids)
sbgnmap.add_glyph(g)
dids[str(entity)] = g.get_id()
for op in net.los:
g = _make_glyph_from_lo(op)
sbgnmap.add_glyph(g)
dids[str(op)] = g.get_id()
for op in net.los:
arcs = _make_arcs_from_lo(op, dids)
for arc in arcs:
sbgnmap.add_arc(arc)
for process in net.processes:
p = _make_glyph_from_process(process)
sbgnmap.add_glyph(p)
dids[str(process)] = p.get_id()
arcs = _make_arcs_from_process(process, dids)
for arc in arcs:
sbgnmap.add_arc(arc)
for modulation in net.modulations:
arc = _make_arc_from_modulation(modulation, dids)
sbgnmap.add_arc(arc)
sbgn.write_file(filename)
ifile = open(filename)
s = ifile.read()
ifile.close()
s = s.replace("sbgn:", "")
s = s.replace(' xmlns:sbgn="http://sbgn.org/libsbgn/0.2"', "")
s = s.replace('."', '.0"')
ofile = open(filename, "w")
ofile.write(s)
ofile.close()
def __init__(self, width, height, pg_x, pg_y):
"""
:param width: total width of final image
:param height: total height of final image
:param pg_x: x coordinate of process glyph
:param pg_y: x coordinate of process glyph
"""
self.sbgn = libsbgn.sbgn()
self.map = libsbgn.map(language=Language.PD)
self.sbgn.set_map(self.map)
self.box = libsbgn.bbox(x=0, y=0, w=width, h=height)
self.map.set_bbox(self.box)
# process glyph size
self.pg_size = PROCESS_GLYPH_SIZE
self.port_in = None
self.port_out = None
self._set_process_glyph(pg_x, pg_y)
def sbgn():
""" Fixture provides sbgn test data via sbgn argument. """
# 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 map
box = libsbgn.bbox(x=0, y=0, w=363, h=253)
sbgn_map.set_bbox(box)
# create some glyphs
# class attribute is named 'class_' ! in glyphs and arcs
# glyphs with labels
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph1")
g.set_label(libsbgn.label(text="Ethanol"))
g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60))
sbgn_map.add_glyph(g)
# glyph with ports (process)
g = libsbgn.glyph(class_=GlyphClass.PROCESS,
id="pn1",
orientation=Orientation.HORIZONTAL)
g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24))
g.add_port(libsbgn.port(x=136, y=180, id="pn1.1"))
g.add_port(libsbgn.port(x=184, y=180, id="pn1.2"))
sbgn_map.add_glyph(g)
# arcs
# create arcs and set the start and end points
a = libsbgn.arc(class_=ArcClass.CONSUMPTION,
source="glyph1",
target="pn1.1",
id="a01")
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
sbgn_map.add_arc(a)
return sbgn
def sbgn():
""" Fixture provides sbgn test data via sbgn argument. """
# 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 map
box = libsbgn.bbox(x=0, y=0, w=363, h=253)
sbgn_map.set_bbox(box)
# create some glyphs
# class attribute is named 'class_' ! in glyphs and arcs
# glyphs with labels
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph1')
g.set_label(libsbgn.label(text='Ethanol'))
g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60))
sbgn_map.add_glyph(g)
# glyph with ports (process)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id='pn1',
orientation=Orientation.HORIZONTAL)
g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24))
g.add_port(libsbgn.port(x=136, y=180, id="pn1.1"))
g.add_port(libsbgn.port(x=184, y=180, id="pn1.2"))
sbgn_map.add_glyph(g)
# arcs
# create arcs and set the start and end points
a = libsbgn.arc(class_=ArcClass.CONSUMPTION, source="glyph1", target="pn1.1", id="a01")
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
sbgn_map.add_arc(a)
return sbgn
def makeSBGNML(net):
iglyph = 0
iarc = 0
sbgn = libsbgn.sbgn()
sbgnmap = libsbgn.map()
language = libsbgn.Language.PD
sbgnmap.set_language(language)
sbgn.set_map(sbgnmap)
dids = {}
for epn in net.getEntities():
iglyph, g = SBGN.makeGlyphFromEntity(epn, iglyph)
sbgnmap.add_glyph(g)
dids[epn.getId()] = g.get_id()
for process in net.getProcesses():
iglyph, p = SBGN.makeGlyphFromProcess(process, iglyph)
sbgnmap.add_glyph(p)
dids[process.getId()] = p.get_id()
iarc, arcs = SBGN.makeArcsFromProcess(process, iarc, dids)
for arc in arcs:
sbgnmap.add_arc(arc)
for modulation in net.getModulations():
iarc, arc = SBGN.makeArcFromModulation(modulation, iarc, dids)
sbgnmap.add_arc(arc)
return sbgn
def makeSBGNML(net):
iglyph = 0
iarc = 0
sbgn = libsbgn.sbgn()
sbgnmap = libsbgn.map()
language = libsbgn.Language.PD
sbgnmap.set_language(language)
sbgn.set_map(sbgnmap);
dids = {}
for epn in net.getEntities():
iglyph, g = SBGN.makeGlyphFromEntity(epn, iglyph)
sbgnmap.add_glyph(g)
dids[epn.getId()] = g.get_id()
for process in net.getProcesses():
iglyph, p = SBGN.makeGlyphFromProcess(process, iglyph)
sbgnmap.add_glyph(p)
dids[process.getId()] = p.get_id()
iarc, arcs = SBGN.makeArcsFromProcess(process, iarc, dids)
for arc in arcs:
sbgnmap.add_arc(arc)
for modulation in net.getModulations():
iarc, arc = SBGN.makeArcFromModulation(modulation, iarc, dids)
sbgnmap.add_arc(arc)
return sbgn
def test_basestring_issue():
"""
This tests issue: https://github.com/matthiaskoenig/libsbgn-python/issues/4
"""
# 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, 100, 100)
sbgn_map.set_bbox(box)
# glyphs with labels
for comp in ("Cytoplasm",):
c_id = comp
c_name = comp
(x, y), (w, h) = (10, 10), (90, 90)
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)
s2xy = {"H2": (20, 20), "O2": (20, 80), "H2O": (80, 60)}
for species, (x, y) in s2xy.items():
s_id = species
s_name = species
glyph_type = GlyphClass.UNSPECIFIED_ENTITY
glyph_type = GlyphClass.SIMPLE_CHEMICAL
(w, h) = (5, 5)
g = libsbgn.glyph(class_=glyph_type, id=s_id, compartmentRef="Cytoplasm")
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)
r_id = "Water"
(x, y), (w, h) = (60, 60), (4, 4)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id=r_id)
g.set_bbox(libsbgn.bbox(x, y, w, h))
in_port = None
for s_id in ("O2", "H2"):
edge_id = "-".join(sorted((s_id, r_id)))
if not in_port:
port_x, port_y = (61, 62)
in_port = libsbgn.port(x=port_x, y=port_y, id="%s__in" % r_id)
g.add_port(in_port)
sref_id = s_id
a = libsbgn.arc(
class_=ArcClass.CONSUMPTION,
target=in_port.get_id(),
source=sref_id,
id="a_%s_%s" % (s_id, r_id),
)
s_x, s_y = s2xy[s_id]
a.set_start(libsbgn.startType(x=s_x, y=s_y))
a.set_end(libsbgn.endType(x=in_port.get_x(), y=in_port.get_y()))
sbgn_map.add_arc(a)
out_port = None
for s_id in ("H2O",):
edge_id = "-".join(sorted((s_id, r_id)))
if not out_port:
port_x, port_y = (63, 62)
out_port = libsbgn.port(x=port_x, y=port_y, id="%s__out" % r_id)
g.add_port(out_port)
sref_id = s_id
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 = s2xy[s_id]
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
f_tmp = tempfile.NamedTemporaryFile(suffix=".sbgn")
sbgn.write_file(f_tmp.name)
def write_sbgn_02(f):
"""Create SBGN document and write to file.
:param f:
:return:
"""
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a bounding box for map
# <bbox x="0" y="0" w="363" h="253"/>
# [1] de novo and set all attributes
# box = libsbgn.bbox()
# box.set_x(0)
# box.set_y(0)
# box.set_w(363)
# box.set_h(253)
# [2] de novo with attributes at creation
box = libsbgn.bbox(x=0, y=0, w=363, h=253)
map.set_bbox(box)
# create some glyphs
# class attribute is named 'class_' ! in glyphs and arcs
"""
<glyph class="simple chemical" id="glyph1">
<label text="Ethanol"/> <!-- fontsize="" etc -->
<!-- Line breaks are allowed in the text attribute -->
<bbox x="40" y="120" w="60" h="60"/>
</glyph>
"""
# glyphs with labels
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph1")
g.set_label(libsbgn.label(text="Ethanol"))
g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph_ethanal")
g.set_label(libsbgn.label(text="Ethanal"))
g.set_bbox(libsbgn.bbox(x=220, y=110, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.MACROMOLECULE, id="glyph_adh1")
g.set_label(libsbgn.label(text="ADH1"))
g.set_bbox(libsbgn.bbox(x=106, y=20, w=108, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph_h")
g.set_label(libsbgn.label(text="H+"))
g.set_bbox(libsbgn.bbox(x=220, y=190, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph_nad")
g.set_label(libsbgn.label(text="NAD+"))
g.set_bbox(libsbgn.bbox(x=40, y=190, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph_nadh")
g.set_label(libsbgn.label(text="NADH"))
g.set_bbox(libsbgn.bbox(x=300, y=150, w=60, h=60))
map.add_glyph(g)
# glyph with ports (process)
g = libsbgn.glyph(class_=GlyphClass.PROCESS,
id="pn1",
orientation=Orientation.HORIZONTAL)
g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24))
g.add_port(libsbgn.port(x=136, y=180, id="pn1.1"))
g.add_port(libsbgn.port(x=184, y=180, id="pn1.2"))
map.add_glyph(g)
# arcs
# create arcs and set the start and end points
a = libsbgn.arc(class_=ArcClass.CONSUMPTION,
source="glyph1",
target="pn1.1",
id="a01")
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION,
source="pn1.2",
target="glyph_nadh",
id="a02")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=300, y=180))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.CATALYSIS,
source="glyph_adh1",
target="pn1",
id="a03")
a.set_start(libsbgn.startType(x=160, y=80))
a.set_end(libsbgn.endType(x=160, y=168))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION,
source="pn1.2",
target="glyph_h",
id="a04")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=224, y=202))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION,
source="pn1.2",
target="glyph_ethanal",
id="a05")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=224, y=154))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.CONSUMPTION,
source="glyph_nad",
target="pn1.1",
id="a06")
a.set_start(libsbgn.startType(x=95, y=202))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
# write to file
sbgn.write_file(f)
def write_sbgn_02(f):
""" Create SBGN document and write to file.
:param f:
:return:
"""
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a bounding box for map
# <bbox x="0" y="0" w="363" h="253"/>
# [1] de novo and set all attributes
# box = libsbgn.bbox()
# box.set_x(0)
# box.set_y(0)
# box.set_w(363)
# box.set_h(253)
# [2] de novo with attributes at creation
box = libsbgn.bbox(x=0, y=0, w=363, h=253)
map.set_bbox(box)
# create some glyphs
# class attribute is named 'class_' ! in glyphs and arcs
'''
<glyph class="simple chemical" id="glyph1">
<label text="Ethanol"/> <!-- fontsize="" etc -->
<!-- Line breaks are allowed in the text attribute -->
<bbox x="40" y="120" w="60" h="60"/>
</glyph>
'''
# glyphs with labels
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph1')
g.set_label(libsbgn.label(text='Ethanol'))
g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_ethanal')
g.set_label(libsbgn.label(text='Ethanal'))
g.set_bbox(libsbgn.bbox(x=220, y=110, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.MACROMOLECULE, id='glyph_adh1')
g.set_label(libsbgn.label(text='ADH1'))
g.set_bbox(libsbgn.bbox(x=106, y=20, w=108, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_h')
g.set_label(libsbgn.label(text='H+'))
g.set_bbox(libsbgn.bbox(x=220, y=190, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_nad')
g.set_label(libsbgn.label(text='NAD+'))
g.set_bbox(libsbgn.bbox(x=40, y=190, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_nadh')
g.set_label(libsbgn.label(text='NADH'))
g.set_bbox(libsbgn.bbox(x=300, y=150, w=60, h=60))
map.add_glyph(g)
# glyph with ports (process)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id='pn1', orientation=Orientation.HORIZONTAL)
g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24))
g.add_port(libsbgn.port(x=136, y=180, id="pn1.1"))
g.add_port(libsbgn.port(x=184, y=180, id="pn1.2"))
map.add_glyph(g)
# arcs
# create arcs and set the start and end points
a = libsbgn.arc(class_=ArcClass.CONSUMPTION, source="glyph1", target="pn1.1", id="a01")
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION, source="pn1.2", target="glyph_nadh", id="a02")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=300, y=180))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.CATALYSIS, source="glyph_adh1", target="pn1", id="a03")
a.set_start(libsbgn.startType(x=160, y=80))
a.set_end(libsbgn.endType(x=160, y=168))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION, source="pn1.2", target="glyph_h", id="a04")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=224, y=202))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION, source="pn1.2", target="glyph_ethanal", id="a05")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=224, y=154))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.CONSUMPTION, source="glyph_nad", target="pn1.1", id="a06")
a.set_start(libsbgn.startType(x=95, y=202))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
# write to file
sbgn.write_file(f)
def test_basestring_issue():
"""
This tests issue: https://github.com/matthiaskoenig/libsbgn-python/issues/4
"""
# 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, 100, 100)
sbgn_map.set_bbox(box)
# glyphs with labels
for comp in ('Cytoplasm', ):
c_id = comp
c_name = comp
(x, y), (w, h) = (10, 10), (90, 90)
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)
s2xy = {'H2': (20, 20), 'O2': (20, 80), 'H2O': (80, 60)}
for species, (x, y) in s2xy.items():
s_id = species
s_name = species
glyph_type = GlyphClass.UNSPECIFIED_ENTITY
glyph_type = GlyphClass.SIMPLE_CHEMICAL
(w, h) = (5, 5)
g = libsbgn.glyph(class_=glyph_type, id=s_id, compartmentRef='Cytoplasm')
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)
r_id = 'Water'
(x, y), (w, h) = (60, 60), (4, 4)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id=r_id)
g.set_bbox(libsbgn.bbox(x, y, w, h))
in_port = None
for s_id in ('O2', 'H2'):
edge_id = "-".join(sorted((s_id, r_id)))
if not in_port:
port_x, port_y = (61, 62)
in_port = libsbgn.port(x=port_x, y=port_y, id="%s__in" % r_id)
g.add_port(in_port)
sref_id = s_id
a = libsbgn.arc(class_=ArcClass.CONSUMPTION,
target=in_port.get_id(),
source=sref_id, id="a_%s_%s" % (s_id, r_id))
s_x, s_y = s2xy[s_id]
a.set_start(libsbgn.startType(x=s_x, y=s_y))
a.set_end(libsbgn.endType(x=in_port.get_x(), y=in_port.get_y()))
sbgn_map.add_arc(a)
out_port = None
for s_id in ('H2O', ):
edge_id = "-".join(sorted((s_id, r_id)))
if not out_port:
port_x, port_y = (63, 62)
out_port = libsbgn.port(x=port_x, y=port_y, id="%s__out" % r_id)
g.add_port(out_port)
sref_id = s_id
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 = s2xy[s_id]
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
f_tmp = tempfile.NamedTemporaryFile(suffix=".sbgn")
sbgn.write_file(f_tmp.name)
def test_create_extension():
sbgn = libsbgn.sbgn()
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
extension = Extension(
"""<renderInformation id="example" programName="SBML Layout" programVersion="3.0"
xmlns="http://projects.eml.org/bcb/sbml/render/level2">
<listOfColorDefinitions>
<colorDefinition id="yelloComp" value="#ffffccff" />
<colorDefinition id="grayComp" value="#e0e0e0ff" />
<colorDefinition id="orange" value="#fa9e2fff" />
<colorDefinition id="blue" value="#2958acff" />
<colorDefinition id="green" value="#378f5cff" />
<colorDefinition id="Color_0" value="#969696" />
<colorDefinition id="Color_1" value="#ff9900" />
<colorDefinition id="Color_2" value="#000000" />
</listOfColorDefinitions>
<listOfGradientDefinitions>
<linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="LinearGradient_0" spreadMethod="reflect">
<stop offset="0%" stop-color="#ccffff" />
<stop offset="100%" stop-color="#ffffff" />
</linearGradient>
<linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="OrangeGradient_0" spreadMethod="reflect">
<stop offset="0%" stop-color="#ffffff" />
<stop offset="100%" stop-color="#fa9e2fff" />
</linearGradient>
<linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="BlueGradient_0" spreadMethod="reflect">
<stop offset="0%" stop-color="#ffffff" />
<stop offset="100%" stop-color="#2958acff" />
</linearGradient>
<linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="GreenGradient_0" spreadMethod="reflect">
<stop offset="0%" stop-color="#ffffff" />
<stop offset="100%" stop-color="#378f5cff" />
</linearGradient>
</listOfGradientDefinitions>
<listOfStyles>
<style idList="glyph0 glyph2 glyph14 glyph34 ">
<g stroke="Color_2" stroke-width="5" fill="yelloComp" />
</style>
<style idList="glyph1">
<g stroke="Color_2" stroke-width="5" fill="grayComp" />
</style>
<style idList="glyph8 glyph23 glyph5 glyph12 glyph21 glyph13 glyph4 glyph6 glyph7 glyph20 glyph22">
<g stroke="orange" stroke-width="2" fill="OrangeGradient_0" />
</style>
<style idList="glyph3 glyph47 glyph10 glyph11">
<g stroke="blue" stroke-width="2" fill="BlueGradient_0" />
</style>
<style idList="glyph32 glyph37 glyph37a glyph31 glyph39 glyph40 glyph36 glyph28 glyph35 glyph27 glyph25 glyph26 glyph9 glyph38 glyph38a glyph29 glyph30 glyph46 glyph33">
<g stroke="green" stroke-width="2" fill="GreenGradient_0" />
</style>
<style idList="a38">
<g stroke="blue" stroke-width="2" />
</style>
</listOfStyles>
</renderInformation>"""
)
map.set_extension(extension)
assert map.get_extension() is not None
extension_str = str(map.get_extension())
assert "<linearGradient" in extension_str
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)
###CREATE SBGN FILE### # import libsbgn and important SBGN types import libsbgnpy.libsbgn as libsbgn from libsbgnpy.libsbgnTypes import Language, GlyphClass, ArcClass, Orientation # create empty sbgn sbgn = libsbgn.sbgn() # create map, set language and set in sbgn map = libsbgn.map() map.set_language(Language.PD) sbgn.set_map(map) #EXAMPLE SBGN COMPONENTS #BE ABLE TO IMPORT SBGN COMPONENTS? # create a bounding box for the map box = libsbgn.bbox(x=0, y=0, w=400, h=300) map.set_bbox(box) # glyphs with labels g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph1') g.set_label(libsbgn.label(text='Ethanol')) g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60)) map.add_glyph(g) g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_ethanal') g.set_label(libsbgn.label(text='Ethanal')) g.set_bbox(libsbgn.bbox(x=220, y=110, w=60, h=60)) map.add_glyph(g)
