MIBiG-bigfam-lda.md

Compute LDA of MiBIG (documents) and bigfam subdomains (words)

pipenv install
pipenv shell
sudo apt install hmmer

mkdir MIBiG
wget https://mibig.secondarymetabolites.org/mibig_gbk_1.4.tar.gz
tar -zxf mibig_gbk_1.4.tar.gz
cd ..

mkdir json
cd temp_scripts
python build_json.py ../MIBiG ../json
python apply_hmmscan.py ../json ../bigfam_models/BiGFAM-v1-domains.hmm
python apply_subdomainscan.py ../json ../bigfam_models/BiGFAM-v1-coredomains.txt ../bigfam_models/subdomains

jupyter notebook

Open and run lda.opynb notebook.

pyLDAviz prepare causes kernel restart Trying different versions

pipenv install numpy==1.11.3 scipy==0.18.1 pandas==0.17.0
pipenv install git+https://github.com/bmabey/pyLDAvis.git#egg=pyLDAvis