Metadata-Version: 1.1
Name: rcgrep
Version: 0.1.0rc1
Summary: Search text files for DNA sequences and their reverse complements
Home-page: http://github.com/dib-lab/rcgrep
Author: Daniel Standage
Author-email: daniel.standage@gmail.com
License: MIT
Description: [![rcgrep build status](https://img.shields.io/travis/dib-lab/rcgrep.svg)](https://travis-ci.org/dib-lab/rcgrep)
        [![Test coverage](https://img.shields.io/codecov/c/github/dib-lab/rcgrep.svg)](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.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
