14225235949

Committed 02 Apr 2025 04:56PM UTC coverage: 90.508% (+0.5%) from 90.054%

Build # 14225235949

Build Type

push

github

Committed by

veghp

Commit Message

Bump to v3.2.14

Run Details

1 of 1 new or added line in 1 file covered. (100.0%)

101 existing lines in 35 files now uncovered.

2994 of 3308 relevant lines covered (90.51%)

0.91 hits per line

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95.0

/dnachisel/builtin_specifications/codon_optimization/BaseCodonOptimizationClass.py

from ..CodonSpecification import CodonSpecification
from python_codon_tables import get_codons_table
import numpy as np
from ...Location import Location
from ...biotools import group_nearby_indices


class BaseCodonOptimizationClass(CodonSpecification):

    best_possible_score = 0  # Don't forget to change in subclasses if needed
    localization_group_spread = 3

    def __init__(self, species=None, location=None, codon_usage_table=None, boost=1.0):
        self.boost = boost
        self.location = Location.from_data(location)
        self.species = species
        self.codon_usage_table = self.get_codons_table(species, codon_usage_table)

    def get_codons(self, problem):
        subsequence = self.location.extract_sequence(problem.sequence)
        if len(subsequence) % 3:
            raise ValueError(
                "Spec. %s is on a window/sequence with size not multiple of 3)"
                % (self.label())
            )
        return [
            subsequence[3 * i : 3 * (i + 1)] for i in range(int(len(subsequence) / 3))
        ]

    @staticmethod
    def get_codons_table(species, codon_usage_table):
        if codon_usage_table is None:
            if species is None:
                raise ValueError(
                    "Provide either an species name or a codon usage table"
                )
            else:
                codon_usage_table = get_codons_table(species)
        return codon_usage_table

    def initialized_on_problem(self, problem, role):
        """Get location from sequence if no location provided."""
        return self._copy_with_full_span_if_no_location(problem)

    def codons_indices_to_locations(self, indices):
        """Convert a list of codon positions to a list of Locations"""
        indices = np.array(indices)
        if self.location.strand == -1:
            indices = sorted(self.location.end - 3 * indices)
            return [
                Location(group[0] - 3, group[-1], strand=-1)
                for group in group_nearby_indices(
                    indices, max_group_spread=self.localization_group_spread
                )
            ]
        else:
            indices = self.location.start + 3 * indices
            return [
                Location(group[0], group[-1] + 3)
                for group in group_nearby_indices(
                    indices, max_group_spread=self.localization_group_spread
                )
            ]

    def get_codons_synonyms(self):
        """Return a dict {"GTG": [GTG, GTC, ...]} of synonymous codons."""
        return {
            codon: [c for c in aa_codons]
            for aa, aa_codons in self.codon_usage_table.items()
            if len(aa) == 1
            for codon in aa_codons
        }

    def get_codons_translations(self):
        """Return a dict {"ATG": "M", "TAG": "*", ...}."""
        return {
            codon: aa
            for aa, aa_codons in self.codon_usage_table.items()
            if len(aa) == 1
            for codon in aa_codons.keys()
        }

    def localized_on_window(self, new_location, start_codon, end_codon):
        """Relocate without changing much."""
        # The "new_location" already has exactly the right span and strand
        # thanks to superclass CodonSpecification
        return self.copy_with_changes(location=new_location)

1	from ..CodonSpecification import CodonSpecification	1✔
2	from python_codon_tables import get_codons_table	1✔
3	import numpy as np	1✔
4	from ...Location import Location	1✔
5	from ...biotools import group_nearby_indices	1✔
6
7
8	class BaseCodonOptimizationClass(CodonSpecification):	1✔
9
10	best_possible_score = 0 # Don't forget to change in subclasses if needed	1✔
11	localization_group_spread = 3	1✔
12
13	def __init__(self, species=None, location=None, codon_usage_table=None, boost=1.0):	1✔
14	self.boost = boost	1✔
15	self.location = Location.from_data(location)	1✔
16	self.species = species	1✔
17	self.codon_usage_table = self.get_codons_table(species, codon_usage_table)	1✔
18
19	def get_codons(self, problem):	1✔
20	subsequence = self.location.extract_sequence(problem.sequence)	1✔
21	if len(subsequence) % 3:	1✔
UNCOV 22	raise ValueError(	×
23	"Spec. %s is on a window/sequence with size not multiple of 3)"
24	% (self.label())
25	)
26	return [	1✔
27	subsequence[3 * i : 3 * (i + 1)] for i in range(int(len(subsequence) / 3))
28	]
29
30	@staticmethod	1✔
31	def get_codons_table(species, codon_usage_table):	1✔
32	if codon_usage_table is None:	1✔
33	if species is None:	1✔
UNCOV 34	raise ValueError(	×
35	"Provide either an species name or a codon usage table"
36	)
37	else:
38	codon_usage_table = get_codons_table(species)	1✔
39	return codon_usage_table	1✔
40
41	def initialized_on_problem(self, problem, role):	1✔
42	"""Get location from sequence if no location provided."""
43	return self._copy_with_full_span_if_no_location(problem)	1✔
44
45	def codons_indices_to_locations(self, indices):	1✔
46	"""Convert a list of codon positions to a list of Locations"""
47	indices = np.array(indices)	1✔
48	if self.location.strand == -1:	1✔
49	indices = sorted(self.location.end - 3 * indices)	1✔
50	return [	1✔
51	Location(group[0] - 3, group[-1], strand=-1)
52	for group in group_nearby_indices(
53	indices, max_group_spread=self.localization_group_spread
54	)
55	]
56	else:
57	indices = self.location.start + 3 * indices	1✔
58	return [	1✔
59	Location(group[0], group[-1] + 3)
60	for group in group_nearby_indices(
61	indices, max_group_spread=self.localization_group_spread
62	)
63	]
64
65	def get_codons_synonyms(self):	1✔
66	"""Return a dict {"GTG": [GTG, GTC, ...]} of synonymous codons."""
67	return {	1✔
68	codon: [c for c in aa_codons]
69	for aa, aa_codons in self.codon_usage_table.items()
70	if len(aa) == 1
71	for codon in aa_codons
72	}
73
74	def get_codons_translations(self):	1✔
75	"""Return a dict {"ATG": "M", "TAG": "*", ...}."""
76	return {	1✔
77	codon: aa
78	for aa, aa_codons in self.codon_usage_table.items()
79	if len(aa) == 1
80	for codon in aa_codons.keys()
81	}
82
83	def localized_on_window(self, new_location, start_codon, end_codon):	1✔
84	"""Relocate without changing much."""
85	# The "new_location" already has exactly the right span and strand
86	# thanks to superclass CodonSpecification
87	return self.copy_with_changes(location=new_location)	1✔

Edinburgh-Genome-Foundry / DnaChisel / 14225235949

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