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Playing around with the human genome and Clojure

branch: master
README.md

jenome

Code for playing around with genome data, human or otherwise.

See my blog posts at eigenhombre.com for many more details.

Testing

lein midje # add --lazytest to automatically retest after updating code

Process a .2bit genome file (convert to FASTA-like plain text in stdout):

First, download some .2bit genome code from e.g. http://hgdownload.cse.ucsc.edu/downloads.html. Or, use resources/sacCer3.2bit.

Then,

lein run <filename.2bit>

See also the commented-out example expressions at the bottom of src/jenome/core.clj.

License

Copyright (C) 2012-2013 John Jacobsen

Distributed under the Eclipse Public License, the same as Clojure.

Disclaimer

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

(Basically, use at your own risk.)

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