Skip to main content

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

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for metasort, version 0.3.6.3
Filename, size File type Python version Upload date Hashes
Filename, size metasort-0.3.6.3.tar.gz (548.9 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page