metasort
Release 0.3.6.3

Filter reads based on taxonomy assignment from OneCodex.

License: MIT
Install: pip install metasort==0.3.6.3

Documentation

# 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/)

Dependencies: 0
Dependent packages: 0
Dependent repositories: 1
Total releases: 14
Latest release: Apr 10, 2015
First release: Apr 9, 2015
Stars: 3
Forks: 2
Watchers: 2
Contributors: 3
Repository size: 1.51 MB
SourceRank: 6