cl-gn: Common Lisp GeneNetwork

/Maybe the last word on accelerated web programming/

In this repo we explore Common Lisp for GeneNetwork.

Hacking

Drop into a development environment with

guix shell

or for a container the more verbose

guix shell -C -D -m manifest.scm

Start the GeneNetwork web server (listening on port 8080) and the slynk REPL server (listening on port 4005) using

sbcl --load run.lisp

If using Emacs, connect to slynk using M-x sly-connect RET localhost RET 4005 RET. Happy Hacking!

genodb genotype database tool

Building and running tests

This repo also includes the genodb CLI tool to manipulate GeneNetwork's genotype databases. To build it, run

sbcl --load build.lisp

To run tests, run

sbcl --script tests.lisp

Usage

Convert a plain text GeneNetwork genotype file BXD.geno to a genodb genotype database bxd using

./genodb import BXD.geno bxd

If the bxd database does not exist, it is created as a directory containing .mdb files. If bxd already exists and contains a matrix, the genotype matrix of BXD.geno is stored in bxd as a new version.

Print meta-information and list versions stored in a genotype database bxd using

./genodb info bxd
Path: bxd/
Versions: 1
Keys: 5606

Version 1
  Dimensions: 7321 × 236

If you add the same file you'll see the database won't grow, even though it contains two identical copies. That is because genodb deduplicates rows.