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... | @@ -55,14 +55,14 @@ make | ... | @@ -55,14 +55,14 @@ make |
55 | ## Train a model | 55 | ## Train a model |
56 | Default usage: | 56 | Default usage: |
57 | ``` bash | 57 | ``` bash |
58 | -python scripts/train.py --featurer=${path_IRSOM}/bin/Featurer -c coding.fasta -n noncoding.fasta --output=output_dir_of_model | 58 | +python ${path_IRSOM}scripts/train.py --featurer=${path_IRSOM}/bin/Featurer -c coding.fasta -n noncoding.fasta --output=output_dir_of_model |
59 | ``` | 59 | ``` |
60 | 60 | ||
61 | The use of multiple fasta files are allowed with this script. | 61 | The use of multiple fasta files are allowed with this script. |
62 | For example, we can create a model with 2 coding fasta files and 3 non-coding fasta files with the following command: | 62 | For example, we can create a model with 2 coding fasta files and 3 non-coding fasta files with the following command: |
63 | 63 | ||
64 | ``` bash | 64 | ``` bash |
65 | -python scripts/train.py --featurer=${path_IRSOM}/bin/Featurer -c coding1.fasta -c coding2.fasta -n noncoding1.fasta -n noncoding2.fasta -n noncoding3.fasta | 65 | +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 |
66 | ``` | 66 | ``` |
67 | 67 | ||
68 | The model parameters can be set by the command parameters: | 68 | The model parameters can be set by the command parameters: |
... | @@ -78,7 +78,7 @@ To keep this files, use the parameter --keep\_features. | ... | @@ -78,7 +78,7 @@ To keep this files, use the parameter --keep\_features. |
78 | 78 | ||
79 | Default usage: | 79 | Default usage: |
80 | ``` bash | 80 | ``` bash |
81 | -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}] | 81 | +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}] |
82 | ``` | 82 | ``` |
83 | 83 | ||
84 | The rejection threshold can be set with the option `--reject`. | 84 | The rejection threshold can be set with the option `--reject`. | ... | ... |
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