DeepBGC: Biosynthetic Gene Cluster detection and classification.
Install DeepBGC
- Run
pip install deepbgc
to install thedeepbgc
python module.
Prerequisities
- Install Python 3.6 (version 3.7 is not supported by TensorFlow yet)
- Install Prodigal and put the
prodigal
binary it on your PATH: https://github.com/hyattpd/Prodigal/releases - Install HMMER and put the
hmmscan
andhmmpress
binaries on your PATH: http://hmmer.org/download.html - Download and extract Pfam database from: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/Pfam-A.hmm.gz
Use DeepBGC
Detection
Detect BGCs in a genomic sequence.
# Show detection help
deepbgc detect --help
# Detect BGCs in a nucleotide sequence
deepbgc detect --model DeepBGCDetector_v0.0.1.pkl --pfam Pfam-A.hmm --output myCandidates/ myInputSequence.fa
# Detect BGCs with >0.9 score in existing Pfam CSV sequence
deepbgc detect --model myModel.pkl --output myStrictCandidates/ -s 0.9 myCandidates/myCandidates.pfam.csv
Classification
Classify BGCs into one or more classes.
# Show classification help
deepbgc classify --help
# Predict biosynthetic class of detected BGCs
deepbgc classify --model RandomForestMIBiGClasses_v0.0.1.pkl --output myCandidates/myCandidates.classes.csv myCandidates/myCandidates.candidates.csv