GEBVtest Software

The GEBV test is a validation procedure described in the Interbull Code of Practice, Appendix X.

This software consists of two programs (gtconvert.py and gebvtest.py) and utility module used by those programs (ibutils.py).

Some sample data is also provided to test the correct functioning of the programs.

Note: In the future, organizations may prefer to prepare the data for the gebvtest.py program directly, bypassing the creation of the legacy file formats and the gtconvert.py program.

Installation

The programs have been tested under Python 2.6, 2.7 and 3.2. As a minimum you will need to have these extra python modules installed on your system: NumPy and, just for Python 2.6, argparse.

Download the attached gebvtest20130131c.zip file.

Create a working directory and unzip the zip file in that directory. Two subdirectories will be created, programs and sample data. Typing

• python gebvtest.py --help

from a command line prompt, from within the programs directory, should print a brief help message if the installation has been successful.

User manuals:

• << public/gtconvert_py >>

• Program gtconvert.py

• Program gebvtest.py

Sample data for program testing

Some sample data for breed HOL and population ABC are available in the sample_data directory. The two programs can be run from the programs directory as follows:

python gtconvert.py -v hol abc ../sample_data
python gebvtest.py -v -m hol abc ../sample_data

In this example data, parameters and output are all in the sample_data directory. Files can be read from other locations and output written to other locations as well. Please consult the help function for further information.

The outputs should match those in the source zip file.

Troubleshooting/FAQ

• Double check your data files and make sure the file formats are ok.
  • In some cases special characters in bull names make the program crash. A hint is to leave out the bull names as they are not used anyway.
  • All your files should contain a field of “country sending this information” and the code should be consistent for all files. Leaving a blank instead of a code for “country sending this information” has the effect that the file is not read.
  • The record type (fist three positions of the file) must correspond to the data. So if your file is a longevity file the record type must be ‘017’ and not ‘717’ or ‘019’ or anything else.
• Make sure to use the -v flag and check the log files carefully (look for files with 0 records, for example)
• If python crashes with an error message:
  • if any "import" statement causes an error, Python or one of the modules is not correctly installed
  • if the gtconvert.py program crashes with an error message that says something about invalid 'utf8' characters, try specifying the '-e iso-8859-1' option (or some other encoding listed on the web page indicated in the --help message) - you may(!) be able to identify input data problems by looking at the program in the area of the line number printed by the error message

  • otherwise, please prepare a zip file with all the inputs and partial outputs (including screen output from gtconvert.py) and email it to interbull@slu.se , clearly showing the exact command line used to launch the program, and pasting in the error message too.

• If bulls seem to be missing or in excess in the candidate or test groups, use -v -m options, but not -C, and check the merged files.