1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
### pyhegp --- Homomorphic encryption of genotypes and phenotypes
### Copyright © 2025 Arun Isaac <arunisaac@systemreboot.net>
###
### This file is part of pyhegp.
###
### pyhegp is free software: you can redistribute it and/or modify it
### under the terms of the GNU General Public License as published by
### the Free Software Foundation, either version 3 of the License, or
### (at your option) any later version.
###
### pyhegp is distributed in the hope that it will be useful, but
### WITHOUT ANY WARRANTY; without even the implied warranty of
### MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
### General Public License for more details.
###
### You should have received a copy of the GNU General Public License
### along with pyhegp. If not, see <https://www.gnu.org/licenses/>.
from hypothesis import strategies as st
from hypothesis.extra.pandas import column, columns, data_frames, range_indexes
import pandas as pd
from scipy.stats import special_ortho_group
from typing import assert_never
from pyhegp.serialization import Summary, is_genotype_metadata_column, is_phenotype_metadata_column
from pyhegp.utils import negate
tabless_printable_ascii_text = st.text(
# Exclude control characters and tab.
st.characters(codec="ascii",
exclude_categories=("Cc",),
exclude_characters=("\t",)),
min_size=1)
chromosomes = tabless_printable_ascii_text
positions = st.integers(min_value=0,
max_value=10*10**9)
references = st.text(st.characters(codec="ascii",
categories=(),
include_characters=("A", "G", "C", "T")),
min_size=1)
sample_names = (tabless_printable_ascii_text
.filter(negate(is_genotype_metadata_column)))
def genotype_metadata(draw, number_of_snps, reference_present):
match list(zip(*draw(st.lists(st.tuples(chromosomes, positions, references)
if reference_present
else st.tuples(chromosomes, positions),
min_size=number_of_snps,
max_size=number_of_snps,
unique=True)))):
case []:
return pd.DataFrame({"chromosome": pd.Series(dtype="str"),
"position": pd.Series(dtype="int")}
| ({"reference": pd.Series(dtype="str")}
if reference_present else {}))
case chromosomes_lst, positions_lst, *references_lst:
return pd.DataFrame({"chromosome": pd.Series(chromosomes_lst, dtype="str"),
"position": pd.Series(positions_lst, dtype="int")}
| ({"reference": pd.Series(*references_lst, dtype="str")}
if reference_present else {}))
case _ as unreachable:
assert_never(unreachable)
@st.composite
def summaries(draw):
stats = draw(data_frames(
columns=columns(["mean", "std"],
dtype="float64",
elements=st.floats(allow_nan=False))))
return Summary(draw(st.integers()),
pd.concat((genotype_metadata(draw,
len(stats),
draw(st.booleans())),
stats),
axis="columns"))
@st.composite
def genotype_frames(draw,
number_of_samples=st.integers(min_value=0,
max_value=10),
reference_present=st.booleans()):
_number_of_samples = draw(number_of_samples)
dosages = draw(data_frames(
columns=columns(draw(st.lists(sample_names,
min_size=_number_of_samples,
max_size=_number_of_samples,
unique=True)),
dtype="float64",
elements=st.floats(min_value=0,
max_value=100,
allow_nan=False))))
return pd.concat((genotype_metadata(draw,
len(dosages),
draw(reference_present)),
dosages),
axis="columns")
phenotype_names = st.lists(tabless_printable_ascii_text
.filter(negate(is_phenotype_metadata_column)),
unique=True)
@st.composite
def phenotype_frames(draw,
number_of_samples=st.integers(min_value=0,
max_value=10)):
_number_of_samples = draw(number_of_samples)
return draw(data_frames(
columns=([column(name="sample-id",
dtype="str",
elements=tabless_printable_ascii_text,
unique=True)]
+ columns(draw(phenotype_names),
dtype="float64",
elements=st.floats(min_value=-1000,
max_value=1000,
allow_nan=False))),
index=range_indexes(min_size=_number_of_samples,
max_size=_number_of_samples)))
@st.composite
def keys(draw, size):
return (special_ortho_group(draw(size),
seed=draw(st.integers(min_value=0,
max_value=2**32-1)))
.rvs())
|
