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/)
1 maintainer
Metadata
1 maintainer
Release files for metasort 0.3.6.3
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| metasort-0.3.6.3.tar.gz | 548.9 kB | Without provenance | Details |
Release files / metasort-0.3.6.3.tar.gz
| Download URL | metasort-0.3.6.3.tar.gz |
|---|---|
| Size | 548.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
9f2bed2d48de97b28b21f0ff4a1bb5fcb58247cf5b3185d5ea845d238e9b1b2b
|
|
BLAKE2b-256 checksum How to use checksums |
2743ffa4e9bc4484460d40bf448956dd38ac67906e39165c44ac4fe24593cd26
|
| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
Security for metasort 0.3.6.3
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