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#!/usr/bin/python3
##
## @file printAnnotation.py
## @brief Prints annotation strings for each element
## @author Akiya Jouraku
##
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
## of libSBML. This program uses the open-source MIT license, as follows:
##
## Copyright (c) 2013-2018 by the California Institute of Technology
## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
## and the University of Heidelberg (Germany), with support from the National
## Institutes of Health (USA) under grant R01GM070923. All rights reserved.
##
## Permission is hereby granted, free of charge, to any person obtaining a
## copy of this software and associated documentation files (the "Software"),
## to deal in the Software without restriction, including without limitation
## the rights to use, copy, modify, merge, publish, distribute, sublicense,
## and/or sell copies of the Software, and to permit persons to whom the
## Software is furnished to do so, subject to the following conditions:
##
## The above copyright notice and this permission notice shall be included in
## all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
## DEALINGS IN THE SOFTWARE.
##
## Neither the name of the California Institute of Technology (Caltech), nor
## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
## of Heidelberg, nor the names of any contributors, may be used to endorse
## or promote products derived from this software without specific prior
## written permission.
## ------------------------------------------------------------------------ -->
##
import sys
import os.path
from libsbml import *
def printAnnotation(sb, id=""):
if not sb.isSetAnnotation():
return
pid = ""
if sb.isSetId():
pid = sb.getId()
print("----- " + sb.getElementName() + " (" + pid
+ ") annotation -----" + "\n")
print(sb.getAnnotationString() + "\n")
print("\n")
def main (args):
"""Usage: printAnnotation filename
"""
if len(args) != 2:
print(main.__doc__)
sys.exit(2)
filename = args[1]
document = readSBML(filename)
errors = document.getNumErrors()
print("filename: " + filename + "\n")
if errors > 0:
document.printErrors()
return errors
# Model
m = document.getModel()
printAnnotation(m)
for i in range(0, m.getNumReactions()):
re = m.getReaction(i)
printAnnotation(re)
# SpeciesReference (Reactant)
for j in range(0, re.getNumReactants()):
rt = re.getReactant(j)
if rt.isSetAnnotation():
print(" ")
printAnnotation(rt, rt.getSpecies())
# SpeciesReference (Product)
for j in range(0, re.getNumProducts()):
rt = re.getProduct(j)
if rt.isSetAnnotation():
print(" ")
printAnnotation(rt, rt.getSpecies())
# ModifierSpeciesReference (Modifiers)
for j in range(0, re.getNumModifiers()):
md = re.getModifier(j)
if md.isSetAnnotation():
print(" ")
printAnnotation(md, md.getSpecies())
# KineticLaw
if re.isSetKineticLaw():
kl = re.getKineticLaw()
if kl.isSetAnnotation():
print(" ")
printAnnotation(kl)
# Parameter
for j in range(0, kl.getNumParameters()):
pa = kl.getParameter(j)
if pa.isSetAnnotation():
print(" ")
printAnnotation(pa)
# Species
for i in range(0, m.getNumSpecies()):
sp = m.getSpecies(i)
printAnnotation(sp)
# Compartments
for i in range(0, m.getNumCompartments()):
sp = m.getCompartment(i)
printAnnotation(sp)
# FunctionDefinition
for i in range (0, m.getNumFunctionDefinitions()):
sp = m.getFunctionDefinition(i)
printAnnotation(sp)
# UnitDefinition
for i in range (0, m.getNumUnitDefinitions()):
sp = m.getUnitDefinition(i)
printAnnotation(sp)
# Parameter
for i in range(0, m.getNumParameters()):
sp = m.getParameter(i)
printAnnotation(sp)
# Rule
for i in range(0, m.getNumRules()):
sp = m.getRule(i)
printAnnotation(sp)
# InitialAssignment
for i in range(0, m.getNumInitialAssignments()):
sp = m.getInitialAssignment(i)
printAnnotation(sp)
# Event
for i in range(0,m.getNumEvents()):
sp = m.getEvent(i)
printAnnotation(sp)
# Trigger
if sp.isSetTrigger():
tg = sp.getTrigger()
if tg.isSetAnnotation():
print(" ")
printAnnotation(tg)
# Delay
if sp.isSetDelay():
dl = sp.getDelay()
if dl.isSetAnnotation():
print(" ")
printAnnotation(dl)
# EventAssignment
for j in range(0,sp.getNumEventAssignments()):
ea = sp.getEventAssignment(j)
if ea.isSetAnnotation():
print(" ")
printAnnotation(ea)
# SpeciesType
for i in range(0,m.getNumSpeciesTypes()):
sp = m.getSpeciesType(i)
printAnnotation(sp)
# Constraints
for i in range(0,m.getNumConstraints()):
sp = m.getConstraint(i)
printAnnotation(sp)
return errors
if __name__ == '__main__':
main(sys.argv)
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