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Diffstat (limited to 'topics')
| -rw-r--r-- | topics/genotype-database.gmi | 19 |
1 files changed, 19 insertions, 0 deletions
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)) +``` |