Get Illumina sequencer metadata from flowcell/machine identifier
Project description
fcid
flow cell ID: parse illumina fastq headers to determine machine and flowcell type Thanks to:
- https://www.biostars.org/p/198143/
- https://github.com/10XGenomics/supernova/blob/master/tenkit/lib/python/tenkit/illumina_instrument.py#L12-L45
- Illumina Techinical Support
Disclaimer: this is not a replacement for proper sequencing run tracking. Disclaimer: PRs welcome to fill gaps! Instrument IDs are less reliable as those are often changed by the sequencing center.
Installation
pip install fcid
# or, for you devs
git clone <this repo> && cd fcid
pip install --editable .
Usage (CLI)
# fcid CABBCANXX
# fcid K11111 --by-machine
# fcid 22C37GLT3
Usage (package)
>>> from fcid import run
>>> run.get_tech_type("CABBCANXX", run.FCIDs)
[['HiSeq 2500'], 'High Output v3 flow cell']
Test
pytest
Deployment
- Update version pyproject.toml
- commit and tag
- push to github and make a release
- check the package deployment action
Project details
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