Chemical Hierarchy Approximation for secondary Metabolism clusters Obtained In Silico.
CHAMOIS is a fast method for predicting chemical features of natural products produced by Biosynthetic Gene Clusters (BGCs) using only their genomic sequence. It can be used to get chemical features from BGCs predicted in silico with tools such as GECCO or antiSMASH.
CHAMOIS is implemented in Python, and supports all versions from Python 3.7 onwards. It requires additional libraries that can be installed directly from PyPI, the Python Package Index.
Clone the repository and install it from the local folder. This will take a little bit of time, since it will download the Pfam HMMs used for annotation and install dependencies:
$ pip install git+https://github.com/zellerlab/CHAMOISNote that CHAMOIS uses HMMER3, which can only run on PowerPC, x86-64 and Aarch64 machines running a POSIX operating system. Therefore, CHAMOIS will work on Linux and OSX, but not on Windows.
Once CHAMOIS is installed, you can run it from the terminal by providing it with one or more GenBank file the genomic records of the BGCs to analyze, and an output path where to write the results in HDF5 format:
chamois predict -i records.gbk -o probas.hdf5The output file can be loaded with the anndata package, and corresponds
to a probability matrix where rows are the input BGCs, and columns are the
ChemOnt classes.
To get a summary for each predicted BGC, use the render command:
chamois render -i probas.hdf5Predictions for each BGC will be shown as a tree with their computed probabilities:
╭─────────────────────────── CP123780.1_cluster1 ──────────────────────────────╮
│ CHEMONTID:0000002 (Organoheterocyclic compounds): 0.823 │
│ ├── CHEMONTID:0000050 (Lactones): 0.638 │
│ └── CHEMONTID:0004140 (Oxacyclic compounds): 0.823 │
│ CHEMONTID:0000012 (Lipids and lipid-like molecules): 0.587 │
│ └── CHEMONTID:0003909 (Fatty Acyls): 0.587 │
│ └── CHEMONTID:0000262 (Fatty acids and conjugates): 0.587 │
│ └── CHEMONTID:0000339 (Unsaturated fatty acids): 0.587 │
│ CHEMONTID:0000264 (Organic acids and derivatives): 0.940 │
│ └── CHEMONTID:0000265 (Carboxylic acids and derivatives): 0.833 │
│ ├── CHEMONTID:0001093 (Carboxylic acid derivatives): 0.679 │
│ ├── CHEMONTID:0001137 (Monocarboxylic acids and derivatives): 0.618 │
│ └── CHEMONTID:0001205 (Carboxylic acids): 0.517 │
│ CHEMONTID:0004150 (Hydrocarbon derivatives): 0.997 │
│ CHEMONTID:0004603 (Organic oxygen compounds): 0.997 │
│ ├── CHEMONTID:0000323 (Organooxygen compounds): 0.994 │
│ │ ├── CHEMONTID:0000129 (Alcohols and polyols): 0.893 │
│ │ │ └── CHEMONTID:0001661 (Secondary alcohols): 0.893 │
│ │ ├── CHEMONTID:0000254 (Ethers): 0.538 │
│ │ └── CHEMONTID:0001831 (Carbonyl compounds): 0.852 │
│ └── CHEMONTID:0003940 (Organic oxides): 0.979 │
╰──────────────────────────────────────────────────────────────────────────────╯Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.
Contributions are more than welcome! See CONTRIBUTING.md
for more details.
This software is provided under the GNU General Public License v3.0 or later. CHAMOIS is developped by the Zeller Lab at the European Molecular Biology Laboratory in Heidelberg and the Leiden University Medical Center in Leiden.