14225166311

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

Build # 14225166311

Build Type

push

github

Committed by

veghp

Commit Message

Switch to Sphinx

Run Details

2994 of 3308 relevant lines covered (90.51%)

0.91 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

77.42

/dnachisel/builtin_specifications/AvoidHeterodimerization.py

try:
    import primer3

    PRIMER3_AVAILABLE = True
except (ImportError, OSError):
    primer3 = None

from ..Specification import Specification, SpecEvaluation


class AvoidHeterodimerization(Specification):
    """Avoid that the (sub)sequence anneals with other primers.

    Parameters
    ----------

    other_primers_sequences
      List of ATGC strings representing the sequences of the other primers
      with which annealing will be avoided.

    tmax
      Maximal melting temperature of the interaction between the (sub)sequence
      and the other_primers_sequences.

    location
      Location of the subsequence to be optimized.

    boost
      Multiplicator for this specification's score when used in a
      multi-objective optimization.
    """

    def __init__(self, other_primers_sequences, tmax=5, location=None, boost=1.0):
        self.other_primers_sequences = other_primers_sequences
        self.tmax = tmax
        self.location = location
        self.boost = boost

    def initialized_on_problem(self, problem, role=None):
        return self._copy_with_full_span_if_no_location(problem)

    def localize(self, location, problem=None):
        if self.location.overlap_region(location) is None:
            return None
        else:
            return self

    def evaluate(self, problem):
        if not PRIMER3_AVAILABLE:
            raise ImportError(
                "Using avoid_heterodimerization requires primer3"
                " installed (pip install primer3-py)"
            )
        if len(self.other_primers_sequences) == 0:
            return SpecEvaluation(
                specification=self,
                problem=problem,
                score=0,
                locations=[self.location],
                message="No existing primer",
            )
        sequence = self.location.extract_sequence(problem.sequence)
        melting_temps = [
            primer3.calcHeterodimer(sequence, other_seq).tm
            for other_seq in self.other_primers_sequences
        ]
        largest_tm = max(melting_temps)
        # hackish penalty to guide optimization:
        penalty = 0.001 * sum(melting_temps) / len(melting_temps)
        score = self.tmax - largest_tm - penalty
        return SpecEvaluation(
            specification=self,
            problem=problem,
            score=score,
            locations=[self.location],
            message="Largest Tm = %.1f " % largest_tm,
        )

    def label_parameters(self):
        return [
            ("primers", len(self.other_primers_sequences)),
            ("tmax", self.tmax),
        ]

1	try:	1✔
2	import primer3	1✔
3
4	PRIMER3_AVAILABLE = True	1✔
5	except (ImportError, OSError):	×
6	primer3 = None	×
7
8	from ..Specification import Specification, SpecEvaluation	1✔
9
10
11	class AvoidHeterodimerization(Specification):	1✔
12	"""Avoid that the (sub)sequence anneals with other primers.
13
14	Parameters
15	----------
16
17	other_primers_sequences
18	List of ATGC strings representing the sequences of the other primers
19	with which annealing will be avoided.
20
21	tmax
22	Maximal melting temperature of the interaction between the (sub)sequence
23	and the other_primers_sequences.
24
25	location
26	Location of the subsequence to be optimized.
27
28	boost
29	Multiplicator for this specification's score when used in a
30	multi-objective optimization.
31	"""
32
33	def __init__(self, other_primers_sequences, tmax=5, location=None, boost=1.0):	1✔
34	self.other_primers_sequences = other_primers_sequences	1✔
35	self.tmax = tmax	1✔
36	self.location = location	1✔
37	self.boost = boost	1✔
38
39	def initialized_on_problem(self, problem, role=None):	1✔
40	return self._copy_with_full_span_if_no_location(problem)	1✔
41
42	def localize(self, location, problem=None):	1✔
43	if self.location.overlap_region(location) is None:	×
44	return None	×
45	else:
46	return self	×
47
48	def evaluate(self, problem):	1✔
49	if not PRIMER3_AVAILABLE:	1✔
50	raise ImportError(	×
51	"Using avoid_heterodimerization requires primer3"
52	" installed (pip install primer3-py)"
53	)
54	if len(self.other_primers_sequences) == 0:	1✔
55	return SpecEvaluation(	1✔
56	specification=self,
57	problem=problem,
58	score=0,
59	locations=[self.location],
60	message="No existing primer",
61	)
62	sequence = self.location.extract_sequence(problem.sequence)	1✔
63	melting_temps = [	1✔
64	primer3.calcHeterodimer(sequence, other_seq).tm
65	for other_seq in self.other_primers_sequences
66	]
67	largest_tm = max(melting_temps)	1✔
68	# hackish penalty to guide optimization:
69	penalty = 0.001 * sum(melting_temps) / len(melting_temps)	1✔
70	score = self.tmax - largest_tm - penalty	1✔
71	return SpecEvaluation(	1✔
72	specification=self,
73	problem=problem,
74	score=score,
75	locations=[self.location],
76	message="Largest Tm = %.1f " % largest_tm,
77	)
78
79	def label_parameters(self):	1✔
80	return [	×
81	("primers", len(self.other_primers_sequences)),
82	("tmax", self.tmax),
83	]

Edinburgh-Genome-Foundry / DnaChisel / 14225166311

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous