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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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