combgc 0.6.4

A tool that aggregates, filters and combines the results of BGC prediction tools: antiSMASH, deepBGC, and GECCO.

comBGC

comBGC is a tool that can be used to combine the results of the prediction tools deepBGC, GECCO, and antiSMASH for detecting bionsynthetic gene clusters (BGCs). It combines the results of all three tools and adds different filters, so only hight quality BGCs are included. Furthermore, a merging step is applied to the datasets. This removes the redundancy and combines the results of the prediction tool. This way no duplicate BGCs are included in the final table.

Installation

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To use comBGC, you first need to create an environment using conda:

conda create -n combgc

Activate the environment

conda activate combgc

and install the required packages using pip

pip install -r requirements.txt

Using comBGC

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To run comBGC and parse the results of multiple BGC prediction tools into a single table you need to specify diffent parameters which can be displayed with using -h :

python3 combgc/comBGC.py --help

Using --helpt gives you an overview of all parameters that can be modified, of which -i, -o, and --cores are required.

comBGC arguments:
    -h, --help              
    -i [PATH(s) [PATH(s) ...]], --input [PATH(s) [PATH(s) ...]] # required
    -o [PATH], --outdir [PATH]                                  # required
    -a [PATH], --antismash_multiple_samples [PATH] 
    -vv, --verbose          
    -v, --version           
    --cores [CORES]                                             # required
    --min_length [LENGTH]   
    --contig_edge [BASES]   
    --sample_metadata [PATH]
    --contig_metadata

• -o, --outdir
• -i, --input path(s) to the required output file(s) of antiSMASH, DeepBGC and/or GECCO these can be:
  - antiSMASH: .gbk and (optional) knownclusterblast/ directory
  - DeepBGC: .bgc.tsv
  - GECCO: .clusters.tsv
  Note: Please provide files from a single sample only. If you would like to summarize multiple samples, please see the --antismash_multiple_samples flag.
• -o, --outdir directory for comBGC output. Default: current directory
• -a, --antismash_multiple_samples directory of antiSMASH output. Should contain subfolders (one per sample). Can only be used if --input is not specified.
• -vv, --verbose increase output verbosity
• -v, --version show version number and exit
• --cores number of CPU cores to use
• --min_length Minimum length [bp] of BGC sequence to keep. Default: 3000 bp
• --contig_edge Exclude BGCs within X bases on the contig edge. Default: 2 bp
• --sample_metadata Path to a TSV file containing sample metadata, e.g., 'path/to/sample_metadata.tsv'. The metadata table must have sample names in the first column and contig IDs in the second column.
• --contig_metadata Path to a TSV file containing contig metadata, e.g., 'path/to/contig_metadata.tsv'. The metadata table must have sample names in the first column and contig IDs in the second column.

Example Usage

python3 combgc/comBGC.py \
-i tests/antismash_example/ECO010-megahit/ECO010-megahit.gbk \
tests/deepbgc_example/ECO010-megahit/ECO010-megahit.bgc.tsv \
tests/gecco_example/ECO010-megahit/ECO010-megahit.clusters.tsv \
-o ./output/ --cores 10

Authors

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This tool was initiated by Jasmin Frangenberg (@jasmezz) and expanded by Tom Richtermeier (@tomrichtermeier), while being supervised by Anan Ibrahim (@Darcy220606)

Funding

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This project was funded by Werner Siemens Foundation grant ‘Palaeobiotechnology’