cl-genomic

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Introduction

cl-genomic is a portable Common Lisp library for processing genomic data, including DNA, RNA and amino-acid sequences, and the biological relationships between them.

Installation

cl-genomic uses ASDF for system definition. Copy or symlink cl-genomic.asd (and optionally cl-genomic-test.asd) to your asdf:central-registry and load cl-genomic with the asdf:load-system function:

(asdf:load-system :cl-genomic)

Tests

To run the unit and regression tests you need to have LIFT installed. Run the tests with the asdf:test-system function:

(asdf:test-system :cl-genomic)

Documentation

See the Lisp docstrings, particularly the package docstrings for an overview. HTML documentation may be generated with the command:

(dxs:document-system :cl-genomic)

at the REPL, provided that CLDOC is installed.

The manual provides an overview of the design philosophy and examples of use.

Dependencies

deoxybyte-systems git://github.com/keithj/deoxybyte-systems.git deoxybyte-utilities git://github.com/keithj/deoxybyte-utilities.git deoxybyte-io git://github.com/keithj/deoxybyte-io.git deoxybyte-unix git://github.com/keithj/deoxybyte-unix.git

cl-ppcre http://weitz.de/cl-ppcre/ PURI http://puri.b9.com/ git://git.b9.com/puri.git CFFI http://common-lisp.net/project/cffi/ Ironclad http://method-combination.net/lisp/ironclad/ git://github.com/froydnj/ironclad.git cl-base64 http://www.cliki.net/cl-base64/ git://git.b9.com/cl-base64.git

Optional dependencies

PowerLoom http://www.isi.edu/isd/LOOM/PowerLoom/

LIFT http://common-lisp.net/project/lift/ git://github.com/gwkkwg/lift.git CLDOC http://common-lisp.net/project/cldoc/