# R/qtl2 LMDB Adapter
## Tags

* assigned: alexm
* priority: medium
* type: feature, documentation
* status: WIP
* keywords: rqtl2, lmdb, adapter, cross

## Description
We want to add support for reading crosses from LMDB.
Currently, R/qtl2 (https://kbroman.org/qtl2/) only supports reading from CSV files.

## Tasks

* [x] Dump genotypes to LMDB
* [x] Dump cross metadata to LMDB
* [-] Create a `read_lmdb_cross` adapter
* [] Dump phenotypes to LMDB

## Using the Adapter

### Dumping the Genotypes
You can find the `lmdb_matrix.py` script here:

=> https://github.com/genenetwork/genenetwork3/blob/main/scripts/lmdb_matrix.py

```sh
guix shell python-click python-lmdb python-wrapper python-numpy -- \
     python lmdb_matrix.py import-genotype \
     <path-to-genotype-file> <path-to-lmdb-store>
```

## Dumping the Cross Metadata

The script can be found here:
=> https://github.com/genenetwork/genenetwork3/pull/235/files   # lmdb_cross_metadata.py

You need to provide a cross file path. The currently supported formats are JSON and YAML.

Example:

```sh
guix shell python-click python-lmdb python-wrapper python-pyyaml -- \
     python dump_metadata.py dump-cross [LMDB_PATH] [CROSS_FILE_PATH] --file-format yaml/json

# Example

python dump_metadata.py dump-cross "./test_lmdb_data" "./cross_file.json"
```

### Running the R/qtl2 LMDB Adapter Script

The script `rqtl_lmdb_adapter.r` can be found here:
=> https://github.com/genenetwork/genenetwork3/pull/235/files   # rqtl_lmdb_adapter.r

```sh
guix shell r r-thor r-rjson r-qtl2 -- \
     Rscript [PATH_TO_ADAPTER_SCRIPT] [LMDB_PATH]

# Example
Rscript https://github.com/genenetwork/genenetwork3/pull/235/files ./lmdb_path


```
### using this with rqtl2 Example

```r
cross <- read_lmdb_cross(LMDB_DB_PATH)
summary(cross)
cat("Is this cross okay", check_cross2(cross), "\n")
warnings() #  enable warnings for the debug purposes  only!
pr <- calc_genoprob(cross)
out <- scan1(pr, cross$pheno, cores=4)
par(mar=c(5.1, 4.1, 1.1, 1.1))
ymx <- maxlod(out)
plot(out, cross$gmap, lodcolumn=1, col="slateblue") # test generating of qtl plots

```


### References
=> https://kbroman.org/qtl2/assets/vignettes/developer_guide.html