From 6de3e6bf27d1abebb98d6f841af70cd617e81dd0 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Wed, 6 Aug 2025 19:01:04 +0100
Subject: Subset to common SNPs.

* pyhegp/pyhegp.py: Import reduce from functools.
(pool_summaries, encrypt_genotype): New functions.
(pool): Use pool_summaries.
(encrypt): Use encrypt_genotype.
* tests/test_pyhegp.py: Import pandas; Summary, read_summary and
read_genotype from pyhegp.serialization.
(test_pool, test_encrypt): New tests.
* test-data/encrypt-test-encrypted-genotype.tsv,
test-data/encrypt-test-genotype.tsv, test-data/encrypt-test-key,
test-data/encrypt-test-summary, test-data/pool-test-complete-summary,
test-data/pool-test-summary1, test-data/pool-test-summary2: New files.
---
 test-data/encrypt-test-encrypted-genotype.tsv | 4 ++++
 test-data/encrypt-test-genotype.tsv           | 5 +++++
 test-data/encrypt-test-key                    | 2 ++
 test-data/encrypt-test-summary                | 6 ++++++
 test-data/pool-test-complete-summary          | 6 ++++++
 test-data/pool-test-summary1                  | 5 +++++
 test-data/pool-test-summary2                  | 7 +++++++
 7 files changed, 35 insertions(+)
 create mode 100644 test-data/encrypt-test-encrypted-genotype.tsv
 create mode 100644 test-data/encrypt-test-genotype.tsv
 create mode 100644 test-data/encrypt-test-key
 create mode 100644 test-data/encrypt-test-summary
 create mode 100644 test-data/pool-test-complete-summary
 create mode 100644 test-data/pool-test-summary1
 create mode 100644 test-data/pool-test-summary2

(limited to 'test-data')

diff --git a/test-data/encrypt-test-encrypted-genotype.tsv b/test-data/encrypt-test-encrypted-genotype.tsv
new file mode 100644
index 0000000..05c5a6c
--- /dev/null
+++ b/test-data/encrypt-test-encrypted-genotype.tsv
@@ -0,0 +1,4 @@
+chromosome	position	sample1	sample2
+chr1	1	0.943532	-0.331281
+chr2	19	0.314511	-0.110427
+chrX	21	0.188706	-0.066256
\ No newline at end of file
diff --git a/test-data/encrypt-test-genotype.tsv b/test-data/encrypt-test-genotype.tsv
new file mode 100644
index 0000000..b64f6d4
--- /dev/null
+++ b/test-data/encrypt-test-genotype.tsv
@@ -0,0 +1,5 @@
+chromosome	position	reference	sample1	sample2
+chr1	1	A	0	1
+chr2	19	G	2	3
+chrX	21	C	4	5
+chrX	22	T	4	5
\ No newline at end of file
diff --git a/test-data/encrypt-test-key b/test-data/encrypt-test-key
new file mode 100644
index 0000000..1ed8e79
--- /dev/null
+++ b/test-data/encrypt-test-key
@@ -0,0 +1,2 @@
+-0.33128118	0.94353208
+-0.94353208	-0.33128118
\ No newline at end of file
diff --git a/test-data/encrypt-test-summary b/test-data/encrypt-test-summary
new file mode 100644
index 0000000..e6d7984
--- /dev/null
+++ b/test-data/encrypt-test-summary
@@ -0,0 +1,6 @@
+# pyhegp summary file version 1
+# number-of-samples 10
+chromosome	position	reference	mean	standard-deviation
+chr1	1	A	0	1
+chr2	19	G	2	3
+chrX	21	C	4	5
\ No newline at end of file
diff --git a/test-data/pool-test-complete-summary b/test-data/pool-test-complete-summary
new file mode 100644
index 0000000..3e9e9ea
--- /dev/null
+++ b/test-data/pool-test-complete-summary
@@ -0,0 +1,6 @@
+# pyhegp summary file version 1
+# number-of-samples 15
+chromosome	position	mean	standard-deviation
+chr1	1	0	0.96362411
+chr2	19	2	2.8908723
+
diff --git a/test-data/pool-test-summary1 b/test-data/pool-test-summary1
new file mode 100644
index 0000000..f63f986
--- /dev/null
+++ b/test-data/pool-test-summary1
@@ -0,0 +1,5 @@
+# pyhegp summary file version 1
+# number-of-samples 10
+chromosome	position	reference	mean	standard-deviation
+chr1	1	A	0	1
+chr2	19	G	2	3
diff --git a/test-data/pool-test-summary2 b/test-data/pool-test-summary2
new file mode 100644
index 0000000..11c02d1
--- /dev/null
+++ b/test-data/pool-test-summary2
@@ -0,0 +1,7 @@
+# pyhegp summary file version 1
+# number-of-samples 5
+chromosome	position	reference	mean	standard-deviation
+chr1	1	A	0	1
+chr2	19	G	2	3
+chrX	21	C	4	5
+chrX	21	T	4	5
-- 
cgit 1.4.1