aegis_sim.parameterization.trait

 1class Trait:
 2    """Genetic trait
 3
 4    Contains data on traits encoded in the genome.
 5    """
 6
 7    def __init__(self, name, cnf, genarch_type, MODIF_GENOME_SIZE, start_position):
 8        def get(key):
 9            return getattr(cnf, f"G_{name}_{key}")
10
11        self.name = name
12        self.start = start_position
13
14        # Relevant if genetic architecture is composite
15        self.evolvable = get("evolvable")
16        self.agespecific = get("agespecific")
17        self.interpreter = get("interpreter")
18        self.initgeno = get("initgeno")
19
20        # Relevant if genetic architecture is modifying
21        self.initpheno = get("initpheno")
22
23        # Relevant under any genetic architecture
24        self.lo = get("lo")
25        self.hi = get("hi")
26
27        assert genarch_type in ("modifying", "composite")
28
29        if genarch_type == "composite":
30
31            # Determine the number of loci encoding the trait
32            if self.evolvable:
33                if self.agespecific is True:  # one locus per age
34                    self.length = cnf.AGE_LIMIT
35                elif self.agespecific is False:  # one locus for all ages
36                    self.length = 1
37                else:  # custom number of loci
38                    self.length = self.agespecific
39            else:  # no loci for a constant trait
40                self.length = 0
41
42            self._validate()
43
44            # Infer positions in the genome
45            # self.start = start
46            # self.end = self.start + self.length
47            # self.slice = slice(self.start, self.end)
48
49            # self.start = cnf.AGE_LIMIT * constants.starting_site(self.name)
50            # self.end = self.start_position + cnf.AGE_LIMIT
51
52        elif genarch_type == "modifying":
53            if name == "neut":
54                self.length = MODIF_GENOME_SIZE
55            else:
56                self.length = 0
57
58        self.end = self.start + self.length
59
60        self.slice = slice(self.start, self.end)
61
62    def _validate(self):
63        """Check whether input parameters are legal."""
64        if not isinstance(self.evolvable, bool):
65            raise TypeError
66
67        if not 0 <= self.initgeno <= 1:
68            raise ValueError
69
70        if self.evolvable:
71            # if not isinstance(self.agespecific, bool):
72            #     raise TypeError
73
74            if self.interpreter not in (
75                "uniform",
76                "exp",
77                "binary",
78                "binary_exp",
79                "binary_switch",
80                "switch",
81                "linear",
82                "single_bit",
83                "const1",
84                "threshold",
85            ):
86                raise ValueError(f"{self.interpreter} is not a valid interpreter type")
87
88            if not 0 <= self.lo <= 1:
89                raise ValueError
90
91            if not 0 <= self.hi <= 1:
92                raise ValueError
93
94    def __len__(self):
95        """Return number of loci used to encode the trait."""
96        return self.length
97
98    def __str__(self):
99        return self.name