Ludovic PLATON

Update README.md

......@@ -6,6 +6,7 @@ The IRSOM tools can be download as follow:
```bash
git clone https://forge.ibisc.univ-evry.fr/lplaton/IRSOM.git
```
IRSOM has been tested on python3.
## Python package
......@@ -48,8 +49,8 @@ python scripts/train.py --featurer=${path_IRSOM}/bin/featurer -c coding1.fasta -
```
The model parameters can be set by the command parameters:
* --dim0=<value> SOM dimension 0 (by default at 10)
* --dim1=<value> SOM dimension 1 (by default at 10).
* --dim0=<value> SOM dimension 0 (by default at 3)
* --dim1=<value> SOM dimension 1 (by default at 3).
* --batch_size=<value> the size of the batch given at each iteration (by default at 10).
* --penality=<value> Coefficient of the regularization term (by default at 0.001).
......@@ -60,7 +61,7 @@ To keep this files, use the parameter --keep\_features.
Default usage:
``` bash
python scripts/predict.py --featurer=${path_IRSOM}/bin/featurer --file=fasta_file.fasta --model=${path_IRSOM}/model/species/ --output=output_dir_of_result
python scripts/predict.py --featurer=${path_IRSOM}/bin/Featurer --file=fasta_file.fasta --model=${path_IRSOM}/model/species/ --output=output_dir_of_result
```
As for the train script, the features are removed by default.
......