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

Project description

ope

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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.

History

0.1.0 (2019-12-11)

  • First release on PyPI.

Project details


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