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Deal with Motifs or Signatures allowing ambiguity in the sequences.
This class contains Schema which deal with Motifs and Signatures at
a higher level, by introducing `don't care` (ambiguity) symbols into
the sequences. For instance, you could combine the following Motifs:
GATC, GATG, GATG, GATT
as all falling under a schema like GAT*, where the star indicates a
character can be anything. This helps us condense a whole ton of
motifs or signatures.
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Imported modules
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from Bio import Alphabet
from Bio.GA import Organism
from Bio.GA.Crossover.Point import SinglePointCrossover
from Bio.GA.Evolver import GenerationEvolver
from Bio.GA.Mutation.Simple import SinglePositionMutation
from Bio.GA.Repair.Stabilizing import AmbiguousRepair
from Bio.GA.Selection.Diversity import DiversitySelection
from Bio.GA.Selection.Tournament import TournamentSelection
from Bio.Seq import MutableSeq
from Pattern import PatternRepository
import random
import sre
import string
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Functions
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matches_schema
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matches_schema
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matches_schema (
pattern,
schema,
ambiguity_character='*',
)
Determine whether or not the given pattern matches the schema.
Arguments:
pattern - A string representing the pattern we want to check for
matching. This pattern can contain ambiguity characters (which are
assumed to be the same as those in the schema). schema - A string schema with ambiguity characters. ambiguity_character - The character used for ambiguity in the schema.
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Classes
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