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
We need set environment variable export BLASTDB=/data/work/yang/Qing/databases/data/nr
Modify default.yaml with path to the above programs
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
Predict using all features
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
Predict using only CCMPred Predictions
feature_gen
parameters:
a config including the feature names.
the feature directory ( this dir of your ccmpred outputs)
the pickled output (default will be tmp_pickle)
python deepcontact/feature_gen.py ./deepcontact/feature_only_ccmpred.yaml ./tmp_feature ./tmp_pickle/feature_only_ccmpred.pkl
python deepcontact/main_only_ccmpred.py ./tmp_pickle/feature_only_ccmpred.pkl ./tmp_output/prediction_only_ccmpred.pkl