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,
Monomers,
Degenerates=None,
Gaps=None,
Complements=None,
Order=None,
Pairs=None,
WeightAdjust=0,
add_lower=True,
):
"""Returns new Alphabet object, minimally initialized with monomers.
Monomers: Dict of monomers, keyed by symbol. Expect 1-letter and
3-letter symbols, name, and molecular weight (in chain).
Degenerate: Dict of degenerate symbol -> monomer mapping.
Gaps: Dict of valid gap symbols.
Complements:Dict of monomer -> complement (optional).
Order: Customary order in which symbols appear. Used by __iter__.
Pairs: Dict of tuples containing valid, non-degenerate pairs.
WeightAdjust: Weight added for terminal residue
add_lower: Whether or not to add lowercase chars (default True)
NOTE: All of Monomers, Degenerates, Gaps, Complements, Order, Pairs
_must_ support keys() and items() if present.
Alphabets should be treated as immutable, though at present there is
no explicit code to enforce this. However, the Alphabet makes
several additional variables on creation, which would need to be
handled carefully if some of the Alphabet's components were changed.
"""
self.Monomers = Monomers
self.Degenerates = Degenerates or {}
self.Gaps = Gaps or {}
self.Complements = Complements or {}
self.Matches = MatchMaker(Monomers, Gaps, Degenerates)
self.Pairs = Pairs or {}
self.Pairs.update(PairMaker(Pairs, Monomers, Gaps, Degenerates))
self._add_order(Order)
self.WeightAdjust = WeightAdjust
if add_lower:
self._add_lowercase()
self._make_all()
self._make_comp_table()
self.GapString = "".join(self.Gaps.keys())
self.stripDegenerate = FunctionWrapper(keep_chars(self.GapString + self.Order))
self.stripBad = FunctionWrapper(keep_chars("".join(self.All.keys())))
self.stripBadAndGaps = FunctionWrapper(
keep_chars("".join(map("".join, [self.Monomers.keys(), self.Degenerates.keys()])))
)
# make inverse degenerates from degenerates
# ensure that lowercase versions also exist
inv_degens = {}
for key, val in self.Degenerates.items():
inv_degens[ImmutableSet(val)] = key
inv_degens[ImmutableSet(val.lower())] = key.lower()
for m in self.Monomers:
inv_degens[ImmutableSet(m)] = m
inv_degens[ImmutableSet(m.lower())] = m.lower()
for m in self.Gaps:
inv_degens[ImmutableSet(m)] = m
self.InverseDegenerates = inv_degens
