Source code for cobra.core.Gene

import re
from warnings import warn
from ast import parse as ast_parse, Name, And, Or, BitOr, BitAnd, \
    BoolOp, Expression, NodeTransformer
from keyword import kwlist

from .Species import Species

keywords = list(kwlist)
keywords.extend(("True", "False"))
keyword_re = re.compile(r"(?=\b(%s)\b)" % "|".join(keywords))
number_start_re = re.compile(r"(?=\b[0-9])")

replacements = (
    (".", "__COBRA_DOT__"),
    ("'", "__COBRA_SQUOTE__"),
    ('"', "__COBRA_DQUOTE__"),
    (":", "__COBRA_COLON__"),
    ("/", "__COBRA_FSLASH__"),
    ("\\", "__COBRA_BSLASH"),
    ("-", "__COBRA_DASH__"),
    ("=", "__COBRA_EQ__")

# functions for gene reaction rules
[docs]def ast2str(expr, level=0, names=None): """convert compiled ast to gene_reaction_rule str expr: str of a gene reaction rule level: internal use only names: optional dict of {} Use this to get a rule str which uses names instead. This should be done for display purposes only. All gene_reaction_rule strings which are computed with should use the id. """ if isinstance(expr, Expression): return ast2str(expr.body, 0, names) \ if hasattr(expr, "body") else "" elif isinstance(expr, Name): return names.get(, if names else elif isinstance(expr, BoolOp): op = expr.op if isinstance(op, Or): str_exp = " or ".join(ast2str(i, level + 1, names) for i in expr.values) elif isinstance(op, And): str_exp = " and ".join(ast2str(i, level + 1, names) for i in expr.values) else: raise TypeError("unsupported operation " + op.__class__.__name) return "(" + str_exp + ")" if level else str_exp elif expr is None: return "" else: raise TypeError("unsupported operation " + repr(expr))
[docs]def eval_gpr(expr, knockouts): """evaluate compiled ast of gene_reaction_rule with knockouts""" if isinstance(expr, Expression): return eval_gpr(expr.body, knockouts) elif isinstance(expr, Name): return not in knockouts elif isinstance(expr, BoolOp): op = expr.op if isinstance(op, Or): return any(eval_gpr(i, knockouts) for i in expr.values) elif isinstance(op, And): return all(eval_gpr(i, knockouts) for i in expr.values) else: raise TypeError("unsupported operation " + op.__class__.__name__) elif expr is None: return True else: raise TypeError("unsupported operation " + repr(expr))
[docs]class GPRCleaner(NodeTransformer): """Parses compiled ast of a gene_reaction_rule and identifies genes Parts of the tree are rewritten to allow periods in gene ID's and bitwise boolean operations""" def __init__(self): NodeTransformer.__init__(self) self.gene_set = set()
[docs] def visit_Name(self, node): if"__cobra_escape__"): =[16:] for char, escaped in replacements: if escaped in =, char) self.gene_set.add( return node
[docs] def visit_BinOp(self, node): self.generic_visit(node) if isinstance(node.op, BitAnd): return BoolOp(And(), (node.left, node.right)) elif isinstance(node.op, BitOr): return BoolOp(Or(), (node.left, node.right)) else: raise TypeError("unsupported operation '%s'" % node.op.__class__.__name__)
[docs]def parse_gpr(str_expr): """parse gpr into AST returns: (ast_tree, {gene_ids})""" str_expr = str_expr.strip() if len(str_expr) == 0: return None, set() for char, escaped in replacements: if char in str_expr: str_expr = str_expr.replace(char, escaped) escaped_str = keyword_re.sub("__cobra_escape__", str_expr) escaped_str = number_start_re.sub("__cobra_escape__", escaped_str) tree = ast_parse(escaped_str, "<string>", "eval") cleaner = GPRCleaner() cleaner.visit(tree) eval_gpr(tree, set()) # ensure the rule can be evaluated return tree, cleaner.gene_set
[docs]class Gene(Species): def __init__(self, id=None, name="", functional=True): """ id: A string. name: String. A human readable name. functional: Boolean. Indicate whether the gene is functional. If it is not functional then it cannot be used in an enzyme complex nor can its products be used. """ Species.__init__(self, id=id, name=name) self.functional = functional
[docs] def remove_from_model(self, model=None, make_dependent_reactions_nonfunctional=True): """Removes the association make_dependent_reactions_nonfunctional: Boolean. If True then replace the gene with 'False' in the gene association, else replace the gene with 'True' .. deprecated :: 0.4 Use cobra.manipulation.delete_model_genes to simulate knockouts and cobra.manipulation.remove_genes to remove genes from the model. """ warn("Use cobra.manipulation.remove_genes instead") if model is not None: if model != self._model: raise Exception("%s is a member of %s, not %s" % (repr(self), repr(self._model), repr(model))) if self._model is None: raise Exception('%s is not in a model' % repr(self)) if make_dependent_reactions_nonfunctional: gene_state = 'False' else: gene_state = 'True' the_gene_re = re.compile('(^|(?<=( |\()))%s(?=( |\)|$))' % re.escape( self._model.genes.remove(self) self._model = None for the_reaction in list(self._reaction): the_reaction._gene_reaction_rule = the_gene_re.sub( gene_state, the_reaction.gene_reaction_rule) the_reaction._genes.remove(self) # Now, deactivate the reaction if its gene association evaluates # to False the_gene_reaction_relation = the_reaction.gene_reaction_rule for other_gene in the_reaction._genes: other_gene_re = re.compile('(^|(?<=( |\()))%s(?=( |\)|$))' % re.escape( the_gene_reaction_relation = other_gene_re.sub( 'True', the_gene_reaction_relation) if not eval(the_gene_reaction_relation): the_reaction.lower_bound = 0 the_reaction.upper_bound = 0 self._reaction.clear()