skimindex.unix
Wrappers plumbum pour les outils CLI installés
dans l'image Docker. Tous les outils supportent le piping via l'opérateur |.
| Submodule | Description |
|---|---|
unix.compress |
pigz, unzip |
unix.ncbi |
datasets, dataformat |
unix.obitools |
37 outils OBITools |
unix.download |
curl |
unix.kmindex |
kmindex — index et requête k-mers |
skimindex.unix
Unix tools wrapper module using plumbum.
Provides Pythonic interfaces to Unix command-line tools and external programs installed in the Docker image.
Submodules
- download: Download utilities (curl)
- compress: Compression tools (pigz, unzip)
- ncbi: NCBI CLI tools (datasets, dataformat)
- obitools: OBITools bioinformatics tools (37 sequence processing commands)
All tools support piping via plumbum's | operator.
Example
from skimindex.unix import compress, ncbi, obitools from plumbum import FG
Compress with pigz
compress.pigz_compress("file.txt") & FG
Download genome from NCBI
ncbi.datasets_download_genome("--taxon", "human") & FG
Process sequences with OBITools
(obitools.obiconvert["input.fasta"] | obitools.obigrep["-s", "^count>10"]) & FG