https://github.com/alejandrogzi/postoga
The post-TOGA processing pipeline
https://github.com/alejandrogzi/postoga
bioinformatics gene-annotation pipeline post-processing
Last synced: about 2 months ago
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The post-TOGA processing pipeline
- Host: GitHub
- URL: https://github.com/alejandrogzi/postoga
- Owner: alejandrogzi
- License: apache-2.0
- Created: 2023-10-05T19:12:27.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2026-01-22T12:41:14.000Z (about 2 months ago)
- Last Synced: 2026-01-23T02:16:45.955Z (about 2 months ago)
- Topics: bioinformatics, gene-annotation, pipeline, post-processing
- Language: Python
- Homepage:
- Size: 4.88 MB
- Stars: 9
- Watchers: 1
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: Changelog.md
- License: LICENSE
Awesome Lists containing this project
README
> [!WARNING]
>
> postoga is dependent from [TOGA2](https://github.com/hillerlab/TOGA2). Any changes in TOGA2 will have a repercusion here. If you found any bug/errors, please report them here.
> This project is in constant development, any desired features are welcome!
# postoga
The post-[TOGA](https://github.com/hillerlab/TOGA2) processing pipeline.
## What's new on version 0.12
> - Changed 'orthology_status' to 'loss_status' in CLI interface
> - Updated main runner and query table maker to use 'loss_status' terminology
## Usage
To use postoga, just:
Clone the repository
```bash
# clone the repository
git clone --recursive https://github.com/alejandrogzi/postoga.git
cd postoga
```
Activate the environment and configure binaries
```bash
# Recommended: bootstrap everything (uv venv + pip install + maturin develop)
./setup_postoga.sh
# Manual alternative using Hatch targets
pip install hatch
make configure
```
Here is a descrption of postoga features:
> [!TIP]
>
> If the only thing you want to do is apply some filters to a TOGA result or convert results to GTF/GFF files, I recommend the following command:
>
> ```bash
> ./postoga.py \
> --togadir /your/TOGA/dir \
> --outdir /your/out/dir \
> -bc [YOUR CLASSES] \
> -br [YOUR STATUS] \
> -bs [YOUR THRESHOLD] \
> -bp [YOUR PARALOG SCORE] \
> -to [YOUR FORMAT GTF/GFF] \
> --depure \
> -L info
> ```
```text
usage: postoga.py [-h] --togadir TOGADIR [-bc ORTHOLOGY_STATUS]
[-br ORTHOLOGY_CLASS] [-bs ORTHOLOGY_SCORE]
[-to {gtf,gff,bed}] [-tg {bed,utr}]
[-bp MIN_PARALOG_SCORE] [-w WITH_ISOFORMS]
[-ext [{query,reference}]] [--outdir OUTDIR]
[--only-table] [--only-convert]
[-L {debug,info,warn,off}] [--depure] [--version]
optional arguments:
-h, --help show this help message and exit
--togadir TOGADIR, -td TOGADIR
Path to TOGA results directory
-bc ORTHOLOGY_STATUS, --by-orthology-status ORTHOLOGY_STATUS
Filter parameter to only include certain orthology
classes (FI, I, PI, UL, M, PM, L, UL)
-br ORTHOLOGY_CLASS, --by-orthology-class ORTHOLOGY_CLASS
Filter parameter to only include certain orthology
relationships (o2o, o2m, m2m, m2m, o2z)
-bs ORTHOLOGY_SCORE, --by-orthology-score ORTHOLOGY_SCORE
Filter parameter to preserve orthology scores greater
or equal to a given threshold (0.0 - 1.0)
-to {gtf,gff,bed}, --to {gtf,gff,bed}
Specify the conversion format for .bed
(query_annotation/filtered) file (gtf, gff3) or just
keep it as .bed (bed)
-tg {bed,utr}, --target {bed,utr}
Specify the .bed input file to used by the program
-bp MIN_PARALOG_SCORE, --by-paralog-score MIN_PARALOG_SCORE
Filter parameter to preserve transcripts with paralog
projection probabilities less or equal to a given
threshold (0.0 - 1.0)
-w WITH_ISOFORMS, --with-isoforms WITH_ISOFORMS
Path to a custom isoform table (default: None)
-ext [{query,reference}], --extract [{query,reference}]
Flag or option to extract sequences (only codon and
protein alignments) from the filtered genes. Can be
'query', 'reference', or just set as a flag (default:
False). When used as a flag extracting 'query'
sequences is assumed.
--outdir OUTDIR, -o OUTDIR
Path to posTOGA output directory
--only-table, -ot Only produce the toga.table file
--only-convert, -oc Only convert the toga.table file to gtf/gff
-L {debug,info,warn,off}, --level {debug,info,warn,off}
Logging verbosity (debug, info, warn, off)
--depure, -d Remove any trace of other postoga runs/files
--version, -v show this help message and exit
```