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Ludovic PLATON
/
IRSOM
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Authored by
Ludovic PLATON
2018-02-09 09:37:11 +0000
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@@ -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
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@@ -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).
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@@ -60,7 +61,7 @@ To keep this files, use the parameter --keep\_features.
Default usage:
```
bash
python scripts/predict.py --featurer
=
${
path_IRSOM
}
/bin/
f
eaturer --file
=
fasta_file.fasta --model
=
${
path_IRSOM
}
/model/species/ --output
=
output_dir_of_result
python scripts/predict.py --featurer
=
${
path_IRSOM
}
/bin/
F
eaturer --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.
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