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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/)

Release history Release notifications

This version
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0.3.6.3

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0.3.6.2

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0.3.6.1

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0.3.6

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0.3.5

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0.3.4

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0.3.3.2

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0.3.3

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0.3.1

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0.3

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0.2

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0.1.2

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0.1.1

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0.1

Download files

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

Filename, size & hash SHA256 hash help File type Python version Upload date
metasort-0.3.6.3.tar.gz (548.9 kB) Copy SHA256 hash SHA256 Source None Apr 10, 2015

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