DeltaSplice

Code for the paper "Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences". All experiments mentioned in the manuscript can be reproduced with the scripts under the experiments/ folder.

Data preparation

1. models for MMSplice:

cd baselines
git clone https://github.com/gagneurlab/MMSplice_paper.git
cd ..

2. models for pangolin:

cd baselines
git clone https://github.com/tkzeng/Pangolin.git
mv Pangolin/pangolin/models/ pangolin_models
cd ..

3. models for spliceai

cd baselines
git clone https://github.com/Illumina/SpliceAI.git
mv SpliceAI/spliceai/models spliceai_models
cd ..

4. data used in this work is avaiable at xxxx

Generate train/test/valid data from bed file

1. Please refer to gene_dataset.tsu.txt for the format of bed file.
2. Change the custom path in config.py
3. Run

python -m Tools.annotate_gene
python -m Tools.generate_data

Run model training/evaluation

1. Please refer to configs under folder tasks for the format of config/test_config/mut_config file
2. Run

python main.py -c path/to/config
## examples
# train a model: python main.py -c tasks/Pretrain_withcons/config
# test a model: python main.py -c tasks/Pretrain_withcons/test_config

Reproduce experiments mentioned in the manuscript

1. All scripts for experiments are under the folder experiments. In each folder, run.sh contains all the command lines. Directly run "bash run.sh" can generate all the results.
2. experiments/9_plot_and_merge.ipynb is used to summarize all the generated results.

Quick start with pretrained model

1. Please refer to VexSeq_snps2exon_ref_dataset.txt for the format of input data.
2. Write the config file following experiments/2_eval_mut/RefSplice_mut_config.py.
3. Generate file with:

python -m Tools.generate_mutdata /path/to/data /path/to/save reference genome
# example
# python -m Tools.generate_mutdata data/VexSeq_snps2exon_ref_dataset.txt data/vexseq/ hg19 

4. Run the valuation with:

python main_mut.py -c /the/path/to/mut_config