From 671b0ac68fee8c4268ed5a48b5256a0bf9da7cd6 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Fri, 3 Jun 2022 18:52:11 +0530
Subject: topics: Document genotype databases.

* topics/genotype-database.gmi: New file.
---
 topics/genotype-database.gmi | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 topics/genotype-database.gmi

(limited to 'topics')

diff --git a/topics/genotype-database.gmi b/topics/genotype-database.gmi
new file mode 100644
index 0000000..c3f7691
--- /dev/null
+++ b/topics/genotype-database.gmi
@@ -0,0 +1,19 @@
+# Genotype database
+
+GeneNetwork has been using a plain text file format to store genotypes. We are now moving to a fast read-optimized genotype database file format built on LMDB.
+=> https://www.symas.com/lmdb Lightning Memory-Mapped Database
+
+To convert a plain text GeneNetwork genotype file `BXD.geno` to a genodb genotype database `bxd`, use the `genodb` CLI tool from cl-gn like so.
+```
+./genodb import BXD.geno bxd
+```
+=> https://git.genenetwork.org/GeneNetwork/cl-gn cl-gn
+
+genenetwork3 includes a tiny Python library to read the built genodb database. Here is a sample invocation reading row 17 from a database at `/tmp/bxd`.
+```
+from gn3 import genodb
+
+with genodb.GenotypeDatabase('/tmp/bxd') as db:
+    matrix = db.matrix()
+    print(matrix.row(17))
+```
-- 
cgit v1.2.3