README.md

# 1. 从GitHub下载安装CIRI-deep环境
```
git clone https://github.com/gyjames/CIRIdeep.git

```
# 安装环境

```
conda create -n  CIRIdeep  python=3.7
source activate CIRIdeep
pip install tensorflow-1.15.1+git06e2e8aa.dtk2404-cp37-cp37m-linux_x86_64.whl
pip install -r requirements.txt
pip install 'h5py<3.0.0' 
pip install protobuf==3.20.1  -i https://pypi.tuna.tsinghua.edu.cn/simple 

```

环境安装包如下：
```
absl-py              2.1.0
astor                0.8.1
certifi              2022.12.7
cycler               0.11.0
gast                 0.2.2
google-pasta         0.2.0
grpcio               1.62.3
h5py                 2.10.0
importlib-metadata   6.7.0
joblib               1.3.2
Keras                2.3.1
Keras-Applications   1.0.8
Keras-Preprocessing  1.1.2
kiwisolver           1.4.5
Markdown             3.4.4
MarkupSafe           2.1.5
matplotlib           3.3.4
numpy                1.19.2
opt-einsum           3.3.0
pandas               1.1.5
Pillow               9.5.0
pip                  22.3.1
protobuf             3.20.1
pyparsing            3.1.2
python-dateutil      2.9.0.post0
pytz                 2024.1
PyYAML               6.0.1
scikit-learn         0.24.2
scipy                1.7.3
setuptools           65.6.3
six                  1.16.0
tensorboard          1.15.0
tensorflow           1.15.1+git06e2e8aa.dtk2404
tensorflow-estimator 1.15.1
termcolor            2.3.0
threadpoolctl        3.1.0
typing_extensions    4.7.1
Werkzeug             2.2.3
wheel                0.38.4
wrapt                1.16.0
zipp                 3.15.0
```



# 测试

## 用CIRI-deep进行预测
```
python CIRIdeep.py predict -geneExp_absmax ./demo/RBPmax_totalRNA.tsv -seqFeature ./demo/cisfeature.tsv -splicing_max ./demo/splicingamount_max.tsv -predict_list ./demo/predict_list.txt -model_path ./models/CIRIdeep.h5 -outdir ./outdir -RBP_dir ./demo/RBPexp_total -splicing_dir ./demo/splicingamount

```
## 用CIRI-deepA进行预测

```
python CIRIdeep.py predict -geneExp_absmax ./demo/RBPmax_polyA.tsv -seqFeature ./demo/cisfeature.tsv -predict_list ./demo/predict_list.txt -model_path ./models/CIRIdeepA.h5 -outdir ./outdir -RBP_dir ./demo/RBPexp_polyA --CIRIdeepA
```



# 参考文档



```
https://github.com/gyjames/CIRIdeep.git
```