CRMIPred (CRM Interaction Predictor)

Related paper:

Yu-Huai Yu+, Wei-Cheng Dai+, Zhi-Hao Jiang+ and Tzu-Hsien Yang* "CRMIPred: identifying the spatial interactions among Drosophila cis-regulatory modules via considering their cross-attended epigenetic profiles", (submitting).

+: These authors contributed equally.

Prepare the Environment

Suggested running environments: Linux Ubuntu 16.04.6, Python 3.8.13

We recommend that you can use the conda package to create a new environment. This will automatically install the required python packages.

Here is an example:

1. Install the Conda package for you system. The installation of the package can be found here.

2. Create the CRMIPred Conda environment. This may take a while, depending on the network status.

conda create -n "CRMIPred" python=3.8.13

3. Activate your CRMIPred Conda environment.

conda activate CRMIPred

Steps to Use CRMIPred

1. Download the codes from the following link and unzip the file. Please skip it if you have done this step.

wget https://cobis-fs.bme.ncku.edu.tw/CRMIPred/CRMIPred.tar.gz

2. Unzip the file.

tar -zxvf CRMIPred.tar.gz

3. Change the working directory.

cd CRMIPred

4. Download the processed epigenetic datasets from the following link.

wget https://cobis-fs.bme.ncku.edu.tw/CRMIPred/Data.tar.gz

5. Unzip the file.

tar -zxvf CRMIPred_Dataset.tar.gz

6. If this is the first time you use CRMIPred, run the following command to install necessary packages.

pip install -r requirements.txt

CRMIPred can also support GPU acceleration. If you want to utilize GPU, please run the following command instead:

pip install -r requirements_gpu.txt

7. Prepare the input Drosophila CRM region pairs (ver. dm6).

   The input CRM pair format MUST followed the following formats:

CRM_[chromosome]_[start1]_[end1]@CRM_[chromosome]_[start2]_[end2]

Important Rule: The start position of the first CRM must be smaller than the start position of the second CRM (start1 < start2).

For example: (as the input file named input_Test.csv)

Note: The input chromosomal regions start from the 5' end.

8. Predict the probability if the given CRM pairs are interacting pairs.

python main.py -i <input_txt_file> -o <output_file_name> -mode <normal|reduced>

Required arguments:

• -i: The input file for CRMIPred.

• -o: The output prediction results.

Optional arguments:

• -mode: 'normal' (default model) or 'reduced' (reduced version model).

Output Results

If we use the following as our inputs with the example command:

python main.py -i input_test.txt -o output_test

** output_test:**

Output format explanation:

• CRM1@CRM2 [interacting probability].