Refactored the code

Updated Python version to 3.9 alongside the dependencies Replaced dvf.py with the one provided on pull request jessieren#29
owsky · May 24, 2023 · a63c010 · a63c010
1 parent d641ea7
commit a63c010
Show file tree

Hide file tree

Showing 36 changed files with 8,211 additions and 1,384,545 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,3 @@
+venv
+.idea
+**/encode
diff --git a/README.md b/README.md
@@ -1,5 +1,17 @@
 # DeepVirFinder: Identifying viruses from metagenomic data by deep learning
 
+## Conda profile
+    conda create -n dvf python=3.9 theano keras scikit-learn Biopython h5py=2.10.0
+    conda activate dvf
+    pip install numpy==1.21  tensorflow-cpu==2.10 tensorflow-directml-plugin
+
+## Training and prediction
+    ./train_models.sh
+    python dvf.py -i ./data/crAssphage.fa -o ./output/ -l 300 -m ./models
+    python dvf.py -i ./data/CRC_meta.fa -o ./output/ -l 300 -m ./models
+
+
+
 Version: 1.0
 
 Authors: Jie Ren, Kai Song, Chao Deng, Nathan Ahlgren, Jed Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin, Fengzhu Sun

diff --git a/test/CRC_meta.fa → data/CRC_meta.fa b/test/CRC_meta.fa → data/CRC_meta.fa
diff --git a/test/crAssphage.fa → data/crAssphage.fa b/test/crAssphage.fa → data/crAssphage.fa