rcgrep 0.1.0rc1

Search text files for DNA sequences and their reverse complements

[](https://travis-ci.org/dib-lab/rcgrep) [](https://codecov.io/github/dib-lab/rcgrep)

# rcgrep

rcgrep: search text files for DNA sequences and their reverse complements

> ME: I just need to search for a sequence in this file real quick. I’ll use `grep`. > > ALSO ME: Oh, the file is bzip2-compressed. Use `bzgrep`. > > ME AGAIN: Oops, I forgot to search for the sequence’s reverse complement as well. Try again. > > ME, 5 MINUTES LATER: This time I want to search the file for 3 sequences and their reverse complements. Invoke `bzgrep` with multiple `-e` flags. > > ME, HEAD ON DESK: Uggghh, `bzgrep` on Linux doesn’t support multiple `-e` flags. Pipe output of `bzcat` to `grep`.

Like many problems in computational biology, searching for DNA sequences in text files is a very simple task that is unnecessarily complicated by a variety of technical details. rcgrep is a lightweight wrapper for the grep command intended to make these irrelevant details disappear as much as possible.

• rcgrep searches not only for the supplied sequence(s) but also for the corresponding reverse complement(s).

• rcgrep supports searching for multiple query sequences simultaneously.

• rcgrep detects and handles .gz and .bz2 files automatically.

• rcgrep is implemented in pure Python (no compilation required), has no non-standard dependencies, supports Python versions 2 and 3, and can be easily installed via a package manager.

## Quick install

The rcgrep command is easily installed from PyPI.

` pip install rcgrep `

Recommended: to make sure rcgrep is installed correctly, run the tests like so.

` pip install pytest pytest --pyargs rcgrep.tests `

## Contact

This project was originally written by Daniel Standage in the [Lab for Data Intensive Biology](http://ivory.idyll.org/lab/) at UC Davis. If you have any questions, feedback, or suggestions, feel free to contact us via the [issue tracker](https://github.com/dib-lab/rcgrep/issues). Or even better, send us a pull request! Contributions from the wider community are welcomed!

## License

rcgrep is Copyright Regents of the University of California, 2017. All the code is freely available for use and re-use under the MIT License. Distribution, modification and redistribution, incorporation into other software, and pretty much everything else is allowed.