Gene Prediction with AUGUSTUS

INTRODUCTION
DATASET
BASIC
CAVEAT
LICENSES

INTRODUCTION

The present version of Augustus allows to run prediction over a minimal dataset to assess how changes in the code may have affected accuracy. To use testing related function, please set TESTING = true within ../src/Makefile. If either this feature is not required or the required libraries are not available, leave/set TESTING = false (default value).

DATASET

The present distribution comes with an unbiased dataset containing 352 genes from chromosome 1 of human genome (hg38).

BASIC

To make testing available, make sure TESTING is enabled. Under such condition normal prediction can be still run instead of testing, invoking Augustus command line as usual.

Dependencies

Please make sure boost-serialization-dev is installed. If it is not the case, try and run:

sudo apt-get update
sudo apt-get install libboost-serialization-dev

In order to have accuracy returned, EVAL should be installed on your machine. Make sure it is the case

Also, joingenes is required component: please build it running make from within auxprogs/joingenes directory.

Running the python3 script executeTestCGP.py has the following software dependency: - Python3

First use

Run the following script located within scripts sub-directory:

python3 executeTestCGP.py --chunks 27 30 47 54 57 80 86 101 118 --run --augustusDir=my_path_to_binaries --workingDir=my_path_to_dataSet

replacing my_path_to_binaries with the path to the directory named bin, containing comparative Augustus executable on your machine and my_path_to_dataSet with the path to data set used for testing (the dataset can be downloaded from DATASET. When done:

python3 executeTestCGP.py --chunks 27 30 47 54 57 80 86 101 118 --eval --evalDir=my_path_to_Eval

replacing my_path_to_Eval with the path to Eval script. In –eval mode, the script computes accuracy for predictions obtained over the data-set during the execution of –run mode. Results are stored in example/cgp12way/ACCURACY.

CAVEAT

Anyone who plans to modify executeTestCGP.py or use part of it, is recommended not to discard the following option, unless really aware of what she or he is doing:

--stopCodonExcludedFromCDS=true

LICENSES

All source code, i.e. - the AUGUSTUS source code (src/.cc, include/.hh) - the scripts (scripts/*.pl) - the auxiliary programs (auxprogs/) - the tree-parser (src/scanner,src/parser) - include latest config files which return the best accuracy so far obtained (pending)

is under the Artistic License.