# Overview
[](https://github.com/EBI-Metagenomics/combined-gene-caller/actions/workflows/test.yml)
[](https://quay.io/repository/microbiome-informatics/combined-gene-caller)
Combined gene caller for MGnify pipeline, to combine predictions of Prodigal and FragGeneScan.
- Free software: Apache Software License 2.0
## Installation
```bash
pip install https://github.com/ebi-metagenomics/combined-gene-caller/archive/main.zip
```
## Usage
To use the project:
```bash
combined_gene_caller --help
usage: MGnify gene caller combiner. This script will merge the gene called by prodigal and fraggenescan (in any order) [-h] -n NAME [-k MASK] [-a PRODIGAL_OUT]
[-b PRODIGAL_FFN] [-c PRODIGAL_FAA] [-d FGS_OUT]
[-e FGS_FFN] [-f FGS_FAA]
[-p {prodigal_fgs,fgs_prodigal}] [-v] [--version]
optional arguments:
-h, --help show this help message and exit
-n NAME, --name NAME basename
-k MASK, --mask MASK Sequence mask file
-a PRODIGAL_OUT, --prodigal-out PRODIGAL_OUT
Stats out prodigal
-b PRODIGAL_FFN, --prodigal-ffn PRODIGAL_FFN
Stats ffn prodigal
-c PRODIGAL_FAA, --prodigal-faa PRODIGAL_FAA
Stats faa prodigal
-d FGS_OUT, --fgs-out FGS_OUT
Stats out FGS
-e FGS_FFN, --fgs-ffn FGS_FFN
Stats ffn FGS
-f FGS_FAA, --fgs-faa FGS_FAA
Stats faa FGS
-p {prodigal_fgs,fgs_prodigal}, --caller-priority {prodigal_fgs,fgs_prodigal}
Caller priority.
-v, --verbose verbose output
--version show program's version number and exit
```
## Development
To run all the tests run:
pytest
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