Ludovic PLATON

Update README.md

......@@ -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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