Ludovic PLATON / IRSOM

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Ludovic PLATON
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...@@ -6,6 +6,7 @@ The IRSOM tools can be download as follow: ...@@ -6,6 +6,7 @@ The IRSOM tools can be download as follow:
6 ```bash 6 ```bash
7 git clone https://forge.ibisc.univ-evry.fr/lplaton/IRSOM.git 7 git clone https://forge.ibisc.univ-evry.fr/lplaton/IRSOM.git
8 ``` 8 ```
9 +IRSOM has been tested on python3.
9 10
10 ## Python package 11 ## Python package
11 12
...@@ -48,8 +49,8 @@ python scripts/train.py --featurer=${path_IRSOM}/bin/featurer -c coding1.fasta - ...@@ -48,8 +49,8 @@ python scripts/train.py --featurer=${path_IRSOM}/bin/featurer -c coding1.fasta -
48 ``` 49 ```
49 50
50 The model parameters can be set by the command parameters: 51 The model parameters can be set by the command parameters:
51 -* --dim0=<value> SOM dimension 0 (by default at 10) 52 +* --dim0=<value> SOM dimension 0 (by default at 3)
52 -* --dim1=<value> SOM dimension 1 (by default at 10). 53 +* --dim1=<value> SOM dimension 1 (by default at 3).
53 * --batch_size=<value> the size of the batch given at each iteration (by default at 10). 54 * --batch_size=<value> the size of the batch given at each iteration (by default at 10).
54 * --penality=<value> Coefficient of the regularization term (by default at 0.001). 55 * --penality=<value> Coefficient of the regularization term (by default at 0.001).
55 56
...@@ -60,7 +61,7 @@ To keep this files, use the parameter --keep\_features. ...@@ -60,7 +61,7 @@ To keep this files, use the parameter --keep\_features.
60 61
61 Default usage: 62 Default usage:
62 ``` bash 63 ``` bash
63 -python scripts/predict.py --featurer=${path_IRSOM}/bin/featurer --file=fasta_file.fasta --model=${path_IRSOM}/model/species/ --output=output_dir_of_result 64 +python scripts/predict.py --featurer=${path_IRSOM}/bin/Featurer --file=fasta_file.fasta --model=${path_IRSOM}/model/species/ --output=output_dir_of_result
64 ``` 65 ```
65 66
66 As for the train script, the features are removed by default. 67 As for the train script, the features are removed by default.
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