Download test data:
wget https://github.com/ablab/nerpa/releases/download/v1.0.0/test_data.tar.gz
tar xzf test_data.tar.gz
Example: five BGCs sequences downloaded from MIBiG and pre-processed with antiSMASH v.3 against five NRPs in the SMILES format (provided a single database tab-separated file)
Run nerpa
nerpa.py -a test_data/MIBiG_subset/genome_predictions --smiles-tsv test_data/MIBiG_subset/structures_info.tsv
Run NRP Generation
python3 main.py --output="./out_detect" --algorithm=replacements ./nerpa_results/latest/
Check out suggested graphs:
cat ./out_detect/compound_000002_BGC0000447.txt
Output format:
For each NRP and BGC alignment graph variants scored in:
{output}/compound_{compound number as in the nerpa files}_BGC{bgc number}.txt
In this file graph variants are separated with \n and stored in this format:
(vertex_name,)+;(vertex_index1, vertex_index2,monomer_bond_name;)+
For example:
aThr/Thr,Dab,Leu,Gln;0,1,AMINO;2,3,AMINO;