Do you need to run tools on FASTA files with gnu parallel, and then parse the results? You need prescription strength Fuckitall!
Project description
ope
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.
Free software: MIT license
Documentation: https://ope.readthedocs.io.
Features
TODO
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.1.0 (2019-12-11)
First release on PyPI.
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