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DeepContact

Installation

  1. Install the following dependencies
  • HHBlits 2.0.16
  • Jackhmmer 3.1b2
  • HHFilter 2.0.16
  • CCMPred
  • FreeContact 1.0.21
  • MetaPsicov 1.02
  • Blast 2.2.6
  • Psipred 4.0
  1. We need set environment variable export BLASTDB=/data/work/yang/Qing/databases/data/nr
  2. Modify default.yaml with path to the above programs
  3. Install python dependencies with
conda env create -f environment.yml
source activate deepcontact-env
pip install --upgrade https://github.com/Lasagne/Lasagne/archive/master.zip

Usage Example

python data-processing/run_pipeline.py default.yaml test.fasta ./tmp_feature
python deepcontact/feature_gen.py ./deepcontact/feature.yaml ./tmp_feature ./tmp_pickle/feature.pkl
python deepcontact/main.py ./tmp_pickle/feature.pkl ./tmp_output/prediction.pkl

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