Avu Tests

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Andrew's ragtag collection of tests

A bunch of tests for making sure my code changes worked as intended. These are mostly worthless now, with the exception of windoweater.

This project is in the buffy CVS:

export CVS_RSH=ssh
cvs -d:ext:YOUR_USERNAME@cvs.biowiki.org:/usr/local/cvs co avu-tests

The tests

bioperl

featurevole

gb

Mapper

misc

sge

Stockholm

windoweater

Basically, we take a segment and annotate it with a random #=GC CONS annotation, then run it through the window{licker,eater},xrate trio. The conservation parameters are such that only a small number of windows (less than 5) will be run through xrate, with the rest getting an all-intergenic annotation.

Look in the Makefile for the comments and test cases.

How to use:

# load system-specific env vars for paths, etc.
. setenv-babylon.bash
# run test, start to finish
make segment.xrate

windowlicker

xrate

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-- Created by: Andrew Uzilov on 18 Dec 2007