python-cogent 1.5.3-2 / usr / share / pyshared / cogent / evolve / predicate.py

#!/usr/bin/env python
"""
Matching motifs: MotifChange("a", "g")
Boolean logic: Any, All, Not (or &, |, ~)

also:
  anypredicate.aliased('shortname')
  UserPredicate(f)
"""

import warnings
import numpy

__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"

class _CallablePredicate(object):
    # A predicate in the context of a particular model
    def __init__(self, pred, model):
        self.model = model
        self.alphabet = model.getAlphabet()
        self.name = repr(pred)
        self.f = pred.interpret(model)
        self.__doc__ = pred.__doc__
    
    def __call__(self, x, y):
        return self.f(x, y)
    
    def __repr__(self):
        return self.name
    
    def asciiArt(self):
        l = len(self.alphabet.getGapMotif())
        rows = []
        for i in range(l):
            row = [a[i] for a in list(self.alphabet)]
            rows.append(' '*(l+1) + ' '.join(row))
        for y in self.alphabet:
            row = []
            for x in self.alphabet:
                if not self.model.isinstantanious(x, y):
                    c = ' '
                elif self(x,y):
                    c = '*'
                else:
                    c = '-'
                row.append(c)
            rows.append(' '.join([y] + row))
        return '\n'.join(rows)
    

class predicate(object):
    def __and__(self, other):
        return All(self, other)
    
    def __or__(self, other):
        return Any(self, other)
    
    def __invert__(self):
        return Not(self)
    
    def __nonzero__(self):
        warnings.warn('alphabet predicate used as truth value. Use only binary operators: &, | and ~', stacklevel=2)
        return True
    
    def __eq__(self, other):
        warnings.warn('Warning: alphabet pair predicate used as value. Use parentheses')
        return self is other
    
    def aliased(self, new_name):
        n = PredicateAlias(new_name, self)
        n.__doc__ = self.__doc__ or repr(self)
        return n
    
    def makeModelPredicate(self, model):
        return _CallablePredicate(self, model)
    

class PredicateAlias(predicate):
    def __init__(self, name, subpredicate):
        self.name = name
        self.subpredicate = subpredicate
    
    def __repr__(self):
        return self.name
    
    def interpret(self, model):
        subpred = self.subpredicate.interpret(model)
        return subpred
    

class _UnaryPredicate(predicate):
    def __init__(self, subpredicate):
        assert isinstance(subpredicate, predicate), subpredicate
        self.subpredicate = subpredicate
        self.__doc__ = repr(self)
    def __repr__(self):
        if hasattr(self, '_op_repr'):
            return "%s(%s)" % (self._op_repr, self.subpredicate)
        else:
            return "%s(%s)" % (self.__class__.__name__, self.subpredicate)
    

class _GenericPredicate(predicate):
    def __init__(self, *subpredicates):
        for p in subpredicates:
            assert isinstance(p, predicate), p
        self.subpredicates = subpredicates
        self.__doc__ = repr(self)
    def __repr__(self):
        if hasattr(self, '_op_repr'):
            return '(%s)' % (' %s ' % self._op_repr).join([repr(p) for p in self.subpredicates])
        else:
            return '%s(%s)' % (self.__class__.__name__, ','.join(['(%s)' % repr(p) for p in self.subpredicates]))
    

# Boolean logic on motif pair predicates

class Not(_UnaryPredicate):
    _op_repr = '~'
    def interpret(self, model):
        subpred = self.subpredicate.interpret(model)
        def call(*args):
            return not subpred(*args)
        call.__doc__ = repr(self)
        return call
    

class All(_GenericPredicate):
    _op_repr = '&'
    def interpret(self, model):
        subpreds = [p.interpret(model) for p in self.subpredicates]
        def call(*args):
            for subpredicate in subpreds:
                if not subpredicate(*args):
                    return False
            return True
        call.__doc__ = repr(self)
        return call
    

class Any(_GenericPredicate):
    _op_repr = '|'
    def interpret(self, model):
        subpreds = [p.interpret(model) for p in self.subpredicates]
        def call(*args):
            for subpredicate in subpreds:
                if subpredicate(*args):
                    return True
            return False
        call.__doc__ = repr(self)
        return call
    

class ModelSays(predicate):
    def __init__(self, name):
        self.name = name
    
    def __repr__(self):
        return self.name
    
    def interpret(self, model):
        return model.getPredefinedPredicate(self.name)
    

class DirectedMotifChange(predicate):
    def __init__(self, from_motif, to_motif,
                diff_at = None):
        
        self.from_motif = from_motif
        self.motiflen = len(from_motif)
        self.to_motif = to_motif
        self.diff_at = diff_at
    
    def __repr__(self):
        if self.diff_at is not None:
            diff = '[%d]' % self.diff_at
        else:
            diff = ''
        return '%s>%s%s' % (self.from_motif, self.to_motif, diff)
    
    def testMotif(self, motifs, query):
        """positions where motif pattern is found in query"""
        positions = set()
        for offset in range(len(query)-self.motiflen+1):
            for (q,ms) in zip(query[offset: offset+self.motiflen], motifs):
                if q not in ms:
                    break
            else:
                positions.add(offset)
        return positions
    
    def testMotifs(self, from_motifs, to_motifs, x, y):
        """"positions where both motifs patterns are found"""
        pre = self.testMotif(from_motifs, x)
        post = self.testMotif(to_motifs, y)
        return pre & post
    
    def interpret(self, model):
        """Make a callable function which implements this predicate
        specificly for 'alphabet'"""
        
        # may be looking for a 2nt pattern in a 3nt alphabet, but not
        # 3nt pattern in dinucleotide alphabet.
        alphabet = model.getAlphabet()
        if alphabet.getMotifLen() < self.motiflen:
            raise ValueError("Alphabet motifs (%s) too short for %s (%s)" %
                (alphabet.getMotifLen(), repr(self), self.motiflen))
        
        resolve = model.MolType.Ambiguities.__getitem__
        
        from_motifs = [resolve(m) for m in self.from_motif]
        to_motifs = [resolve(m) for m in self.to_motif]
        def call(x, y):
            diffs = [X!=Y for (X,Y) in zip(x, y)]
            matches = []
            for posn in self.testMotifs(from_motifs, to_motifs, x, y):
                diff = list(numpy.nonzero(diffs[posn:posn+self.motiflen])[0])
                if diff and self.diff_at is None or diff == [self.diff_at]:
                    matches.append(posn)
            return len(matches) == 1
        call.__doc__ = repr(self)
        return call
    

class UndirectedMotifChange(DirectedMotifChange):
    def __repr__(self):
        if self.diff_at is not None:
            diff = '[%d]' % self.diff_at
        else:
            diff = ''
        return '%s/%s%s' % (self.from_motif, self.to_motif, diff)
    
    def testMotifs(self, from_motifs, to_motifs, x, y):
        preF = self.testMotif(from_motifs, x)
        postF = self.testMotif(to_motifs, y)
        preR = self.testMotif(from_motifs, y)
        postR = self.testMotif(to_motifs, x)
        return (preF & postF) | (preR & postR)
    

def MotifChange(x, y=None, forward_only=False, diff_at=None):
    if y is None:
        y = ''
        for i in range(len(x)):
            if i == diff_at or diff_at is None:
                y += '?'
            else:
                y += x[i]
    if forward_only:
        return DirectedMotifChange(x, y, diff_at=diff_at)
    else:
        return UndirectedMotifChange(x, y, diff_at=diff_at)

class UserPredicate(predicate):
    def __init__(self, f):
        self.f = f
    def __repr__(self):
        return 'UserPredicate(%s)' % (
                getattr(self.f, '__name__', None) or repr(self.f))
    def interpret(self, model):
        return self.f
    

silent = ModelSays('silent')
replacement = ModelSays('replacement')

def parse(rule):
    if ':' in rule:
        (label, rule) = rule.split(':')
    else:
        label = None
    if '@' in rule:
        (rule, diff_at) = rule.split('@')
        diff_at = int(diff_at)
    else:
        diff_at = None
    
    if '>' in rule or '/' in rule:
        forward_only = '>' in rule
        rule = rule.replace('>', '/')
        (x,y) = rule.split('/')
        if not y: y = None
        
        pred = MotifChange(x, y, forward_only, diff_at)
    else:
        pred = ModelSays(rule)
    
    if label:
        pred = pred.aliased(label)
    return pred