fuckitall

Do you need to run tools on FASTA files with gnu parallel, and then parse the results? You need prescription strength Fuckitall!


Keywords
fuckitall
License
MIT
Install
pip install fuckitall==0.1.0

Documentation

ope

https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat Documentation Status

Abstracts away running gnu-parallel on tools with FASTA input and provides parsers for some common formats produced by said tools.

Example usage:

ope parallel -j 4 [query.pep.fa] hmmscan --domtblout [results.tbl] -E 1e-05 -o /dev/null /store/biodb/Pfam-A.hmm /dev/stdin

Hence, the only gnu-parallel flag one needs to worry about is -j for the number of cores to use. Note that you also need to set the input in the actual tool invocation as /dev/stdin.

Features

  • TODO

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.