| Name | metapyrodigal JSON |
| Version |
1.4.1
JSON |
| download |
| home_page | None |
| Summary | Pyrodigal cli optimized for metagenomic data |
| upload_time | 2025-01-24 21:44:16 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT License
Copyright (c) 2023 Cody Martin
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE. |
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| VCS |
 |
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|
| requirements |
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# README
## Introduction
This library is a simple wrapper of [pyrodigal](https://github.com/althonos/pyrodigal), which is a cythonized implementation of [prodigal](https://github.com/hyattpd/Prodigal/) that is orders of magnitudes faster.
Pyrodigal is mostly written for single genomes or FASTA files, so this tool was created to batch process metagenomic-scale datasets. Metagenomic data usually consists of large number of genome files for MAGs. Additionally, viral metagenomic datasets tend to store all single-scaffold viruses in a single file, which tends to be much larger than a typical single-genome FASTA file.
This tool uses different load balancing strategies to parallelize pyrodigal over large amounts of files (MAGs) or FASTA files that have a large number of scaffolds (viruses).
## Installation
## Install versioned releases
```bash
pip install metapyrodigal
```
## Install from source
```bash
git clone https://github.com/cody-mar10/metapyrodigal.git
cd metapyrodigal
pip install .
```
## Usage
This tool will overwrite the `pyrodigal` binary, so you can use the metagenome-focused binary that I created.
The help page from `pyrodigal -h` looks like this:
```txt
usage: pyrodigal [-h] (-i FILE [FILE ...] | -d DIR) [-o DIR] [-c INT] [--genes] [--virus-mode] [-x STR]
[--allow-unordered]
Find ORFs from query genomes using pyrodigal v3.5.2, the cythonized prodigal API
options:
-h, --help show this help message and exit
-i FILE [FILE ...], --input FILE [FILE ...]
fasta file(s) of query genomes (can use unix wildcards)
-d DIR, --input-dir DIR
directory of fasta files to process
-o DIR, --outdir DIR output directory (default: /storage2/scratch/ccmartin6/software/metapyrodigal)
-c INT, --max-cpus INT
maximum number of threads to use (default: 1)
--genes use to also output the nucleotide genes .ffn file
--virus-mode use pyrodigal-gv to activate the virus models (default: False)
-x STR, --extension STR
genome FASTA file extension if using -d/--input-dir (default: fna)
--allow-unordered for a single file input, this allows the protein ORFs to be written per scaffold as
available. All protein ORFs for each scaffold will be in order, but the scaffolds will not
necessarily be in the same order as in the input nucleotide file. **This is useful if you
are extremely memory limited,** since the default strategy can lead to the ORFs being
stored in memory for awhile before writing to file as the original scaffold order is
maintained. NOTE: This is about 20 percent faster, so it is recommended to use this if the
order of scaffolds does not matter.
```
`-i` and `-d` are mutually exclusive but one of them must be provided.
The output files have the same basename as the input file. Protein FASTA files will have the extension `.faa`, and nucleotide gene FASTA files will have the extension `.ffn`. For example:
```bash
pyrodigal -i GENOME.fna
```
will output `GENOME.faa`
Raw data
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