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Filter reads based on taxonomy assignment from OneCodex.

Project description

# Metasort

A Digital Health Hack Weekend Project using OneCodex API.

Filter reads based on taxonomy assignment from OneCodex.

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

## CLI

set your OneCodex 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/)

Project details


Download files

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Source Distribution

metasort-0.3.6.3.tar.gz (548.9 kB view hashes)

Uploaded source

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