14225166311

Committed 02 Apr 2025 04:53PM UTC coverage: 90.508% (+0.5%) from 90.054%

Build # 14225166311

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veghp

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91.67

/dnachisel/builtin_specifications/AvoidStopCodons.py

from ..biotools import translate
from ..Location import Location
from ..Specification import SpecEvaluation
from .CodonSpecification import CodonSpecification

from Bio.Data import CodonTable


class AvoidStopCodons(CodonSpecification):
    """Do not introduce any new stop codon in that frame.

    This can be used for research purposes, to avoid breaking a reading frame
    when editing it with quasi-synonymous mutations.
    """

    def __init__(self, genetic_table="Standard", location=None, boost=1.0):
        self.genetic_table = genetic_table
        self.boost = boost
        self.location = Location.from_data(location)

    def initialized_on_problem(self, problem, role):
        """Get translation from the sequence if it is not already set."""
        return self._copy_with_full_span_if_no_location(problem)

    def localized_on_window(self, new_location, start_codon, end_codon):
        return self.copy_with_changes(location=new_location)

    def evaluate(self, problem):
        location = (
            self.location
            if self.location is not None
            else Location(0, len(problem.sequence))
        )
        subsequence = location.extract_sequence(problem.sequence)
        translation = translate(subsequence, table=self.genetic_table)
        errors_locations = [
            self.codon_index_to_location(index)
            for index in range(len(translation))
            if translation[index] == "*"
        ]
        return SpecEvaluation(
            self,
            problem,
            score=-len(errors_locations),
            locations=errors_locations,
            message=(
                "All OK."
                if len(errors_locations) == 0
                else "Stop codons found at indices %s" % errors_locations
            ),
        )

    def __str__(self):
        """Represent."""
        return "AvoidStopCodons(%s)" % self.location

    def __str__(self):
        """Represent."""
        return "AvoidStopCodons(%s)" % self.location

1	from ..biotools import translate	1✔
2	from ..Location import Location	1✔
3	from ..Specification import SpecEvaluation	1✔
4	from .CodonSpecification import CodonSpecification	1✔
5
6	from Bio.Data import CodonTable	1✔
7
8
9	class AvoidStopCodons(CodonSpecification):	1✔
10	"""Do not introduce any new stop codon in that frame.
11
12	This can be used for research purposes, to avoid breaking a reading frame
13	when editing it with quasi-synonymous mutations.
14	"""
15
16	def __init__(self, genetic_table="Standard", location=None, boost=1.0):	1✔
17	self.genetic_table = genetic_table	1✔
18	self.boost = boost	1✔
19	self.location = Location.from_data(location)	1✔
20
21	def initialized_on_problem(self, problem, role):	1✔
22	"""Get translation from the sequence if it is not already set."""
23	return self._copy_with_full_span_if_no_location(problem)	1✔
24
25	def localized_on_window(self, new_location, start_codon, end_codon):	1✔
26	return self.copy_with_changes(location=new_location)	1✔
27
28	def evaluate(self, problem):	1✔
29	location = (	1✔
30	self.location
31	if self.location is not None
32	else Location(0, len(problem.sequence))
33	)
34	subsequence = location.extract_sequence(problem.sequence)	1✔
35	translation = translate(subsequence, table=self.genetic_table)	1✔
36	errors_locations = [	1✔
37	self.codon_index_to_location(index)
38	for index in range(len(translation))
39	if translation[index] == "*"
40	]
41	return SpecEvaluation(	1✔
42	self,
43	problem,
44	score=-len(errors_locations),
45	locations=errors_locations,
46	message=(
47	"All OK."
48	if len(errors_locations) == 0
49	else "Stop codons found at indices %s" % errors_locations
50	),
51	)
52
53	def __str__(self):	1✔
54	"""Represent."""
55	return "AvoidStopCodons(%s)" % self.location	×
56
57	def __str__(self):	1✔
58	"""Represent."""
59	return "AvoidStopCodons(%s)" % self.location	×

Edinburgh-Genome-Foundry / DnaChisel / 14225166311

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