def _valid_sbml (self, xml):
if not self._valid_xml (xml):
return False, None
sbml = SBMLReader().readSBMLFromString(xml.decode("utf-8"))
if sbml.getNumErrors() > 0:
for i in range (0, sbml.getNumErrors()):
logging.getLogger(__name__).info("SBML BAD: " + sbml.getError(i).getMessage())
return False, None
return True, sbml
class GEMtractor:
"""Main class for the GEMtractor
It reads an SBML file, trims entities, and extracts the encoded network.
:param sbml_file: path to the SBML file
:type sbml_file: str
"""
def __init__(self, sbml_file):
self.__GENE_ASSOCIATION_PATTERN = re.compile(r".*GENE_ASSOCIATION:([^<]+) *<.*", re.DOTALL)
self.__GENE_LIST_PATTERN = re.compile(r".*GENE_LIST: *([^ <][^<]*)<.*", re.DOTALL)
self.__EXPRESSION_PARSER = self.__get_expression_parser ()
self.__logger = logging.getLogger(__name__)
self.__reaction_gene_map = {}
self.__sbml_file = sbml_file
self.__fbc_plugin = None
self.__logger.debug("reading sbml file " + self.__sbml_file)
self.sbml = SBMLReader().readSBML(self.__sbml_file)
if self.sbml.getNumErrors() > 0:
e = []
for i in range (0, self.sbml.getNumErrors()):
e.append (self.sbml.getError(i).getMessage())
raise IOError ("model seems to be invalid: " + str (e))
def __get_expression_parser (self):
"""
get a parser to parse gene-association strings of reactions
:return: the expression parser
:rtype: `pyparsing:ParserElement <https://pyparsing-docs.readthedocs.io/en/latest/pyparsing.html#pyparsing.ParserElement>`_
"""
variables = pp.Word(pp.alphanums + "_-.")
condition = pp.Group(variables)
return pp.infixNotation(condition,[("and", 2, pp.opAssoc.LEFT, ),("or", 2, pp.opAssoc.LEFT, ),])
def _parse_expression (self, expression):
"""
parse a gene-association expression
uses the expression parser from :func:`_GEMtractor__get_expression_parser`
:param expression: the gene-association expression
:type expression: str
:return: the parse result
:rtype: `pyparsing:ParseResults <https://pyparsing-docs.readthedocs.io/en/latest/pyparsing.html#pyparsing.ParseResults>`_
"""
try:
return self.__EXPRESSION_PARSER.parseString(expression.lower (), True)
except pp.ParseException as e:
raise InvalidGeneExpression ("cannot parse expression: >>" + expression + "<< -- " + getattr(e, 'message', repr(e)))
def _unfold_complex_expression (self, parseresult):
"""
unfold a gene-association parse result
takes a parse result and unfolds it to a list of alternative gene complexes, which can catalyze a certain reaction
:param parseresult: the result of the expression parser
:type parseresult: `pyparsing:ParseResults <https://pyparsing-docs.readthedocs.io/en/latest/pyparsing.html#pyparsing.ParseResults>`_
:return: the list of gene-complexes catalyzing
:rtype: list of :class:`.network.genecomplex.GeneComplex`
"""
if isinstance(parseresult, pp.ParseResults):
if len(parseresult) == 1:
return self._unfold_complex_expression (parseresult[0])
if len(parseresult) > 1 and len(parseresult) % 2 == 1:
# this is a chain of ANDs/ORs
# make sure it's only ANDs or only ORs
for i in range (0, math.floor (len(parseresult) / 2) - 1):
if parseresult[2*i+1] != parseresult[2*i+3]:
# if it's mixed we'll raise an error
self.__logger.critical('and/or mixed in expression: ' + str(parseresult[1]))
raise NotImplementedError ('and/or mixed in expression: ' + str(parseresult[1]))
logic = None
if parseresult[1] == "and":
logic = True
elif parseresult[1] == "or":
logic = False
else:
self.__logger.critical('neither and nor or -> do not understand: ' + str(parseresult[1]))
raise NotImplementedError ('neither and nor or -> do not understand: ' + str(parseresult[1]))
# parse the first subterm
term_combination = self._unfold_complex_expression (parseresult[0])
# from the second subterm, it depends on the logic-connection on how to combine subterms
for i in range(2, len(parseresult), 2):
if logic:
# it's ANDed -> so every previous item needs to be connected to every next item
newterms = self._unfold_complex_expression (parseresult[i])
# ~ tmp = []
for a in term_combination:
for b in newterms:
a.add_genes (b)
# ~ tmp.append (str(a)+" and "+str (b))
# ~ term_combination = tmp
else:
# just add them to the list as alternatives
term_combination += self._unfold_complex_expression (parseresult[i])
return term_combination
else:
self.__logger.critical('unexpected expression: ' + str(parseresult))
raise NotImplementedError ('unexpected expression: ' + str(parseresult))
else:
return [GeneComplex (Gene (parseresult))]
def _extract_genes_from_sbml_notes (self, annotation, default):
"""
extract the genes from a free-text sbml note
expects the gene associations as
.. code-block:: xml
<p>GENE_ASSOCIATION: a and (b or c)</p>
:param annotation: the annotation string
:param default: the default to return if no gene-associations were found
:type annotation: str
:type default: str
:return: the gene-associations
:rtype: string
"""
m = re.match (self.__GENE_ASSOCIATION_PATTERN, annotation)
if m:
g = m.group (1).strip()
if len (g) > 0:
return g
return default
def _overwrite_genes_in_sbml_notes (self, new_genes, reaction):
"""
set the gene-associations for a note in an sbml reaction
overwrites it, if it was set already
:param new_genes: the new gene-associations
:param reaction: the sbml reaction
:type new_genes: str
:type reaction: `libsbml:Reaction <http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_reaction.html>`_
"""
m = re.match (self.__GENE_ASSOCIATION_PATTERN, reaction.getNotesString())
if m:
reaction.setNotes (reaction.getNotesString().replace (m.group (1), new_genes))
else:
self.__logger.debug('no gene notes to update: ' + reaction.getId ())
# TODO
# also update the GENE_LIST using __GENE_LIST_PATTERN
# but for this we need the list of genes here (not only the logic expression)
def get_gene_product_annotations (self, gene):
"""
get the annotations of a gene product
if the document is annotated using the `FBC package <http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/fbc>`_ there is good chance we'll find more information about a gene in the gene-product's annotations
:param gene: the label gene product of interest
:type gene: str
:return: the annotations of the gene-product labeled `gene` or None if there are no such annotations
:rtype: xml str
"""
if self.__fbc_plugin is not None:
gp = self.__fbc_plugin.getGeneProductByLabel (gene)
if gp is not None:
return self.__fbc_plugin.getGeneProductByLabel (gene).getAnnotationString()
return None
def get_reaction_annotations (self, reactionid):
"""
get the annotations of an sbml reaction
:param reactionid: the identifier of the reaction in the sbml document
:type reactionid: str
:return: the annotations of that reaction
:rtype: xml str
"""
return self.sbml.getModel().getReaction (reactionid).getAnnotationString ()
def get_sbml (self, filter_species = [], filter_reactions = [], filter_genes = [], filter_gene_complexes = [], remove_reaction_enzymes_removed = True, remove_ghost_species = False, discard_fake_enzymes = False, remove_reaction_missing_species = False, removing_enzyme_removes_complex = True):
""" Get a filtered SBML document from the model file
this parses the SBML file, applies the trimming according to the arguments, and returns the trimmed model
:param filter_species: species identifiers to get rid of
:param filter_reactions: reaction identifiers to get rid of
:param filter_genes: enzyme identifiers to get rid of
:param filter_gene_complexes: enzyme-complex identifiers to get rid of, every list-item should be of format: 'A + B + gene42'
:param remove_reaction_enzymes_removed: should we remove a reaction if all it's genes were removed?
:param remove_ghost_species: should species be removed, that do not participate in any reaction anymore - even though they might be required in other entities?
:param discard_fake_enzymes: should fake enzymes (implicitly assumes enzymes, if no enzymes are annotated to a reaction) be removed?
:param remove_reaction_missing_species: remove a reaction if one of the participating genes was removed?
:param removing_enzyme_removes_complex: if an enzyme is removed, should also all enzyme complexes be removed in which it participates?
:type filter_species: list of str
:type filter_reactions: list of str
:type filter_genes: list of str
:type filter_gene_complexes: list of str
:type remove_reaction_enzymes_removed: bool
:type remove_ghost_species: bool
:type discard_fake_enzymes: bool
:type remove_reaction_missing_species: bool
:type removing_enzyme_removes_complex: bool
:return: the SBML document
:rtype: `libsbml:SBMLDocument <http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_s_b_m_l_document.html>`_
"""
self.__logger.debug("processing sbml model from " + self.__sbml_file)
model = self.sbml.getModel()
name = model.getName ()
if name is None or len (name) < 1:
name = model.getId()
model.setId (model.getId() + "_gemtracted_ReactionNetwork")
model.setName ("GEMtracted ReactionNetwork of " + name)
self.__logger.info("got proper sbml model")
self.__fbc_plugin = model.getPlugin ("fbc")
self.__logger.debug("append a note")
Utils.add_model_note (model, filter_species, filter_reactions, filter_genes, filter_gene_complexes, remove_reaction_enzymes_removed, remove_ghost_species, discard_fake_enzymes, remove_reaction_missing_species, removing_enzyme_removes_complex)
if filter_species is None:
filter_species = []
if filter_reactions is None:
filter_reactions = []
if filter_genes is None:
filter_genes = []
if filter_gene_complexes is None:
filter_gene_complexes = []
if len(filter_species) > 0 or len(filter_reactions) > 0 or len(filter_genes) > 0 or len(filter_gene_complexes) > 0 or discard_fake_enzymes:
try:
#TODO dc modified?
self.__logger.debug("filtering things")
for n in range (model.getNumReactions () - 1, -1, -1):
reaction = model.getReaction (n)
if filter_reactions is not None and reaction.getId () in filter_reactions:
model.removeReaction (n)
continue
if filter_species is not None:
for sn in range (reaction.getNumReactants() -1, -1, -1):
s = reaction.getReactant(sn).getSpecies()
if s in filter_species:
if remove_reaction_missing_species:
model.removeReaction (n)
raise BreakLoops
reaction.removeReactant (sn)
for sn in range (reaction.getNumProducts() -1, -1, -1):
s = reaction.getProduct(sn).getSpecies()
if s in filter_species:
if remove_reaction_missing_species:
model.removeReaction (n)
raise BreakLoops
reaction.removeProduct (sn)
for sn in range (reaction.getNumModifiers() -1, -1, -1):
s = reaction.getModifier(sn).getSpecies()
if s in filter_species:
if remove_reaction_missing_species:
model.removeReaction (n)
raise BreakLoops
reaction.removeModifier (sn)
if filter_genes is not None:
current_genes = self._get_genes (reaction)
self.__logger.debug("current genes: " + self._implode_genes (current_genes) + " - reaction: " + reaction.getId ())
if len(current_genes) < 1:
self.__logger.info("did not find genes in reaction " + reaction.getId ())
raise NotImplementedError ("did not find genes in reaction " + reaction.getId ())
self.__logger.info(discard_fake_enzymes)
if discard_fake_enzymes and len(current_genes) == 1 and "reaction_" in current_genes[0].get_id ():
model.removeReaction (n)
continue
# if len(current_genes) == 1 and current_genes[0] == reaction.getId ():
final_genes = []
for g in current_genes:
# ~ print (g.get_id())
# ~ print (g.genes)
if g.get_id () not in filter_genes and g.get_id () not in filter_gene_complexes and not (removing_enzyme_removes_complex and g.contains_one_of (filter_genes)):
# ~ print (g.get_id() + " will be in model")
final_genes.append (g)
if len (final_genes) < 1:
if remove_reaction_enzymes_removed:
model.removeReaction (n)
continue
else:
final_genes = [Gene (reaction.getId ())]
# should we update the genes in the model?
if (len (final_genes) != len (current_genes)):
self._set_genes_in_sbml (final_genes, reaction)
self.__reaction_gene_map[reaction.getId ()] = final_genes
if reaction.getNumReactants() + reaction.getNumModifiers() + reaction.getNumProducts() == 0:
model.removeReaction (n)
if len(filter_species) > 0 and remove_ghost_species:
for n in range (model.getNumSpecies () - 1, -1, -1):
species = model.getSpecies (n)
if species.getId () in filter_species:
model.removeSpecies (n)
except BreakLoops:
pass
return self.sbml
def _set_genes_in_sbml (self, genes, reaction):
"""
set the genes of a reaction in an sbml model
tries to set the genes using the `FBC package <http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/fbc>`_, if supported, otherwise sets the genes in the reaction's notes.
if genes already exist the will be overwritten...
:param genes: the new list of gene associations
:param reaction: the reaction to annotate
:type genes: list of :class:`.network.genecomplex.GeneComplex`
:type reaction: `libsbml:Reaction <http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_reaction.html>`_
"""
rfbc = reaction.getPlugin ("fbc")
if rfbc is not None:
gpa = rfbc.getGeneProductAssociation()
if gpa is not None:
g = self._implode_genes (genes)
gpa.setAssociation(FbcAssociation_parseFbcInfixAssociation (g, self.__fbc_plugin))
else:
self.__logger.debug('no fbc to update: ' + reaction.getId ())
self._overwrite_genes_in_sbml_notes (self._implode_genes (genes), reaction)
def _implode_genes (self, genes):
"""
implode a list of genes into a proper logical expression
basically joins the list with `or`, making sure every item is enclosed in brackets
:param genes: the list of optional genes
:type genes: list of :class:`.network.genecomplex.GeneComplex`
:return: the logical expression (genes joined using 'or')
:rtype: str
"""
r = "("
for g in genes:
r += str (g.to_sbml_string ()) + " or "
return r[:-4] + ")"
def _get_genes (self, reaction):
"""
get the genes associated to a reaction
Will cache the gene associations. If there is nothing in cache, it will run :func:`_GEMtractor__find_genes`, :func:`_parse_expression`, and :func:`_unfold_complex_expression` to find them.
:param reaction: the SBML S-Base reaction
:type reaction: `libsbml:Reaction <http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_reaction.html>`_
:return: list of GeneComplexes catalyzing the reaction
:rtype: list of :class:`.network.genecomplex.GeneComplex`
"""
if reaction.getId () not in self.__reaction_gene_map:
self.__reaction_gene_map[reaction.getId ()] = self._unfold_complex_expression(self._parse_expression(self.__find_genes (reaction)))
return self.__reaction_gene_map[reaction.getId ()]
def __find_genes (self, reaction):
"""
Look for genes associated to a reaction.
Will check if there are annotations using the
`FBC package <http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/fbc>`_,
otherwise it will evaluate the reactions' notes.
If there are still no valid gene associations, the function assumes there is an undocumented catalyst and falls back to a gene with the reaction's identifier (prefixed with 'reaction\_').
:param reaction: the SBML S-Base reaction
:type reaction: `libsbml:Reaction <http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_reaction.html>`_
:return: the gene associations
:rtype: str
"""
rfbc = reaction.getPlugin ("fbc")
if rfbc is not None:
gpa = rfbc.getGeneProductAssociation()
if gpa is not None:
return gpa.getAssociation().toInfix()
else:
self.__logger.debug('no association: ' + reaction.getId ())
else:
self.__logger.debug('no fbc: ' + reaction.getId ())
return self._extract_genes_from_sbml_notes (reaction.getNotesString(), "reaction_" + reaction.getId ())
def extract_network_from_sbml (self):
"""
Extract the Network from the SBML model
Will go through the SBML file and convert the (remaining) entities into our own network structure.
:return: the network (after optional trimming)
:rtype: :class:`.network.network.Network`
"""
if self.sbml.getNumErrors() > 0:
raise IOError ("model seems to be invalid")
model = self.sbml.getModel()
self.__logger.info ("extracting network from " + model.getId ())
network = Network ()
species = {}
for n in range (0, model.getNumSpecies()):
s = model.getSpecies (n)
species[s.getId ()] = network.add_species (s.getId (), s.getName ())
for n in range (0, model.getNumReactions()):
if n % 100 == 0:
self.__logger.info ("processing reaction " + str (n))
reaction = model.getReaction(n)
# TODO: reversible?
#r = Reaction (reaction.getId (), reaction.getName ())
r = network.add_reaction (reaction.getId (), reaction.getName ())
if reaction.isSetReversible ():
r.reversible = reaction.getReversible ()
current_genes = self._get_genes (reaction)
self.__logger.debug("current genes: " + self._implode_genes (current_genes) + " - reaction: " + reaction.getId ())
if len(current_genes) < 1:
self.__logger.debug("did not find genes in reaction " + reaction.getId ())
raise NotImplementedError ("did not find genes in reaction " + reaction.getId ())
network.add_genes (r, current_genes)
for sn in range (0, reaction.getNumReactants()):
s = reaction.getReactant(sn).getSpecies()
r.add_input (species[s])
for sn in range (0, reaction.getNumProducts()):
s = reaction.getProduct(sn).getSpecies()
r.add_output (species[s])
self.__logger.info ("extracted network")
return network