DeepBGC - Biosynthetic Gene Cluster detection and classification
Project description
# DeepBGC: Biosynthetic Gene Cluster detection and classification.
## Install DeepBGC
- Run `pip install deepbgc` to install the `deepbgc` 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` and `hmmpress` 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.
```bash
# 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.
```bash
# 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
```
## Install DeepBGC
- Run `pip install deepbgc` to install the `deepbgc` 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` and `hmmpress` 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.
```bash
# 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.
```bash
# 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
```
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