blob: 13c321e466b577726b5bb1d4612f00dac9300fbb (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
|
# 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 and column 13 from a database at `/tmp/bxd`.
```
from gn3 import genodb
with genodb.GenotypeDatabase('/tmp/bxd') as db:
matrix = db.matrix()
print(matrix.row(17))
print(matrix.column(13))
```
|
