def test_keep_chars(self): """keep_chars returns a string containing only chars in keep""" f = keep_chars('ab c3*[') self.assertEqual(f(''), '') #empty self.assertRaises(AttributeError, f, None) #None #one character, case sensitive self.assertEqual(f('b'), 'b') self.assertEqual(f('g'), '') self.assertEqual(f('xyz123'), '3') self.assertEqual(f('xyz 123'), ' 3') #more characters, case sensitive self.assertEqual(f('kjbwherzcagebcujrkcs'), 'bcabcc') self.assertEqual(f('f[ffff*ff*fff3fff'), '[**3') # case insensitive f = keep_chars('AbC', False) self.assertEqual(f('abcdef'), 'abc') self.assertEqual(f('ABCDEF'), 'ABC') self.assertEqual(f('aBcDeF'), 'aBc')
def test_keep_chars(self): """keep_chars returns a string containing only chars in keep""" f = keep_chars('ab c3*[') self.assertEqual(f(''),'') #empty self.assertRaises(AttributeError,f,None) #None #one character, case sensitive self.assertEqual(f('b'),'b') self.assertEqual(f('g'),'') self.assertEqual(f('xyz123'),'3') self.assertEqual(f('xyz 123'),' 3') #more characters, case sensitive self.assertEqual(f('kjbwherzcagebcujrkcs'),'bcabcc') self.assertEqual(f('f[ffff*ff*fff3fff'),'[**3') # case insensitive f = keep_chars('AbC',False) self.assertEqual(f('abcdef'),'abc') self.assertEqual(f('ABCDEF'),'ABC') self.assertEqual(f('aBcDeF'),'aBc')
def test_keep_chars(self): """keep_chars returns a string containing only chars in keep""" f = keep_chars("ab c3*[") self.assertEqual(f(""), "") # empty self.assertRaises(AttributeError, f, None) # None # one character, case sensitive self.assertEqual(f("b"), "b") self.assertEqual(f("g"), "") self.assertEqual(f("xyz123"), "3") self.assertEqual(f("xyz 123"), " 3") # more characters, case sensitive self.assertEqual(f("kjbwherzcagebcujrkcs"), "bcabcc") self.assertEqual(f("f[ffff*ff*fff3fff"), "[**3") # case insensitive f = keep_chars("AbC", False) self.assertEqual(f("abcdef"), "abc") self.assertEqual(f("ABCDEF"), "ABC") self.assertEqual(f("aBcDeF"), "aBc")
def __init__(self, chars, name=None, invert_charset=False, strip_f=strip, default_char=None): """Returns new CharFilter object.""" self.Chars = chars self.Name = name self.Invert = invert_charset if invert_charset: if default_char: trans_table = trans_all(chars, default_char) self.Filter = lambda s: s.translate(trans_table) else: self.Filter = exclude_chars(chars) else: if default_char: trans_table = trans_except(chars, default_char) self.Filter = lambda s: s.translate(trans_table) else: self.Filter = keep_chars(chars) self.stripF = strip_f
def __init__(self, motifset, Gap=IUPAC_gap, Missing=IUPAC_missing,\ Gaps=None, Sequence=None, Ambiguities=None, label=None, Complements=None, Pairs=None, MWCalculator=None, \ add_lower=False, preserve_existing_moltypes=False, \ make_alphabet_group=False, ModelSeq=None): """Returns a new MolType object. Note that the parameters are in flux. Currently: motifset: Alphabet or sequence of items in the default alphabet. Does not include degenerates. Gap: default gap symbol Missing: symbol for missing data Gaps: any other symbols that should be treated as gaps (doesn't have to include Gap or Missing; they will be silently added) Sequence: Class for constructing sequences. Ambiguities: dict of char:tuple, doesn't include gaps (these are hard-coded as - and ?, and added later. label: text label, don't know what this is used for. Unnecessary? Complements: dict of symbol:symbol showing how the non-degenerate single characters complement each other. Used for constructing on the fly the complement table, incl. support for mustPair and canPair. Pairs: dict in which keys are pairs of symbols that can pair with each other, values are True (must pair) or False (might pair). Currently, the meaning of GU pairs as 'weak' is conflated with the meaning of degenerate symbol pairs (which might pair with each other but don't necessarily, depending on how the symbol is resolved). This should be refactored. MWCalculator: f(seq) -> molecular weight. add_lower: if True (default: False) adds the lowercase versions of everything into the alphabet. Slated for deletion. preserve_existing_moltypes: if True (default: False), does not set the MolType of the things added in **kwargs to self. make_alphabet_group: if True, makes an AlphabetGroup relating the various alphabets to one another. ModelSeq: sequence type for modeling Note on "Degenerates" versus "Ambiguities": self.Degenerates contains _only_ mappings for degenerate symbols, whereas self.Ambiguities contains mappings for both degenerate and non-degenerate symbols. Sometimes you want one, sometimes the other, so both are provided. """ self.Gap = Gap self.Missing = Missing self.Gaps = frozenset([Gap, Missing]) if Gaps: self.Gaps = self.Gaps.union(frozenset(Gaps)) self.label = label #set the sequence constructor if Sequence is None: Sequence = ''.join #safe default string constructor elif not preserve_existing_moltypes: Sequence.MolType = self self.Sequence = Sequence #set the ambiguities ambigs = {self.Missing:tuple(motifset)+(self.Gap,),self.Gap:(self.Gap,)} if Ambiguities: ambigs.update(Ambiguities) for c in motifset: ambigs[c] = (c,) self.Ambiguities = ambigs #set Complements -- must set before we make the alphabet group self.Complements = Complements or {} if make_alphabet_group: #note: must use _original_ ambiguities here self.Alphabets = AlphabetGroup(motifset, Ambiguities, \ MolType=self) self.Alphabet = self.Alphabets.Base else: if isinstance(motifset, Enumeration): self.Alphabet = motifset elif max(len(motif) for motif in motifset) == 1: self.Alphabet = CharAlphabet(motifset, MolType=self) else: self.Alphabet = Alphabet(motifset, MolType=self) #set the other properties self.Degenerates = Ambiguities and Ambiguities.copy() or {} self.Degenerates[self.Missing] = ''.join(motifset)+self.Gap self.Matches = make_matches(motifset, self.Gaps, self.Degenerates) self.Pairs = Pairs and Pairs.copy() or {} self.Pairs.update(make_pairs(Pairs, motifset, self.Gaps, \ self.Degenerates)) self.MWCalculator = MWCalculator #add lowercase characters, if we're doing that if add_lower: self._add_lowercase() #cache various other data that make the calculations faster self._make_all() self._make_comp_table() # a gap can be a true gap char or a degenerate character, typically '?' # we therefore want to ensure consistent treatment across the definition # of characters as either gap or degenerate self.GapString = ''.join(self.Gaps) strict_gap = "".join(set(self.GapString) - set(self.Degenerates)) self.stripDegenerate = FunctionWrapper( keep_chars(strict_gap+''.join(self.Alphabet))) self.stripBad = FunctionWrapper(keep_chars(''.join(self.All))) to_keep = set(self.Alphabet) ^ set(self.Degenerates) - set(self.Gaps) self.stripBadAndGaps = FunctionWrapper(keep_chars(''.join(to_keep))) #make inverse degenerates from degenerates #ensure that lowercase versions also exist if appropriate inv_degens = {} for key, val in self.Degenerates.items(): inv_degens[frozenset(val)] = key.upper() if add_lower: inv_degens[frozenset(''.join(val).lower())] = key.lower() for m in self.Alphabet: inv_degens[frozenset(m)] = m if add_lower: inv_degens[frozenset(''.join(m).lower())] = m.lower() for m in self.Gaps: inv_degens[frozenset(m)] = m self.InverseDegenerates = inv_degens #set array type for modeling alphabets try: self.ArrayType = self.Alphabet.ArrayType except AttributeError: self.ArrayType = None #set modeling sequence self.ModelSeq = ModelSeq