GitHub - Phelimb/metasort: A Digital Health Hack Weekend Project using OneCodex API. Filter reads based on taxonomy assignment from OneCodex.

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A Digital Health Hack Weekend Project using OneCodex API. Filter reads based on taxonomy assignment from OneCodex.

MIT license

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Name		Name	Last commit message	Last commit date
Latest commit History 74 Commits
metasort		metasort
tests		tests
.gitignore		.gitignore
.travis.yml		.travis.yml
LICENSE.txt		LICENSE.txt
Procfile		Procfile
README		README
requirements.txt		requirements.txt
setup.py		setup.py
webapp.py		webapp.py

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# Metasort

A Digital Health Hack Weekend Project using One Codex API.

Filter reads based on taxonomy assignment from One Codex.

Upload a Fast(a/q) file and download individual files sorted by species.

## CLI

set your One Codex API key

export ONE_CODEX_API_KEY=f8xxxxxxxxxxx78

source venv/bin/activate
pip install metasort

metasort seq.fq /path/to/outdir

example output:

wc -l /path/to/outdir/*.fq | sort -n -k1 | tail
    19648 /path/to/outdir/Cellular organisms.fq
    30016 /path/to/outdir/Staphylococcus aureus subsp. aureus.fq
    81680 /path/to/outdir/Bacteria.fq
   126364 /path/to/outdir/Staphylococcus epidermidis.fq
   398684 /path/to/outdir/Staphylococcus.fq
  2030880 /path/to/outdir/Firmicutes.fq
  3195432 /path/to/outdir/Staphylococcus aureus.fq


## Web

Usage:

    pip install -r requirements
    python webapp.py

Live demo here:

[https://genome-sort.herokuapp.com/](https://genome-sort.herokuapp.com/)