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/)
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
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
metasort-0.3.6.3.tar.gz
(548.9 kB
view hashes)