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Ludovic PLATON
/
IRSOM
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Authored by
Ludovic PLATON
2018-06-29 12:04:38 +0000
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bbf37eea29c99d221d8d691f3a37cc417b59f460
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@@ -55,14 +55,14 @@ make
## Train a model
Default usage:
```
bash
python scripts/train.py --featurer
=
${
path_IRSOM
}
/bin/Featurer -c coding.fasta -n noncoding.fasta --output
=
output_dir_of_model
python
${
path_IRSOM
}
scripts/train.py --featurer
=
${
path_IRSOM
}
/bin/Featurer -c coding.fasta -n noncoding.fasta --output
=
output_dir_of_model
```
The use of multiple fasta files are allowed with this script.
For example, we can create a model with 2 coding fasta files and 3 non-coding fasta files with the following command:
```
bash
python scripts/train.py --featurer
=
${
path_IRSOM
}
/bin/Featurer -c coding1.fasta -c coding2.fasta -n noncoding1.fasta -n noncoding2.fasta -n noncoding3.fasta
python
${
path_IRSOM
}
scripts/train.py --featurer
=
${
path_IRSOM
}
/bin/Featurer -c coding1.fasta -c coding2.fasta -n noncoding1.fasta -n noncoding2.fasta -n noncoding3.fasta
```
The model parameters can be set by the command parameters:
...
...
@@ -78,7 +78,7 @@ 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
[
--reject
=
${
rejection_threshold
}
]
python
${
path_IRSOM
}
/
scripts/predict.py --featurer
=
${
path_IRSOM
}
/bin/Featurer --file
=
fasta_file.fasta --model
=
${
path_IRSOM
}
/model/species/ --output
=
output_dir_of_result
[
--reject
=
${
rejection_threshold
}
]
```
The rejection threshold can be set with the option
`--reject`
.
...
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