Warning
postoga is dependent from 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!
The post-TOGA processing pipeline.
- Changed 'orthology_status' to 'loss_status' in CLI interface
- Updated main runner and query table maker to use 'loss_status' terminology
To use postoga, just:
Clone the repository
# clone the repository
git clone --recursive https://github.com/alejandrogzi/postoga.git
cd postogaActivate the environment and configure binaries
# Recommended: bootstrap everything (uv venv + pip install + maturin develop)
./setup_postoga.sh
# Manual alternative using Hatch targets
pip install hatch
make configureHere 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:
./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 infousage: 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