Program gebvtest.py - User Manual

UNDER CONSTRUCTION!

Information about the program:

The program gebvtest.py performs the GEBV validation tests for one breed-population combination, for all traits. At the end of the program a zip file is created with the input files and the result file, ready for submission to the ITBC. The ITBC will perform some additional data checks and re-run the program to check the results. The result file is a new file735 format file, which is a modification and extension of the previous file731 format file.

For information about installation and sample data for testing the program, see public/GEBVtest_software.

Input files (from gtconvert.py OR prepared by the organization):

• traits - GEBV test options file(Format: traits)

• file300Cf - national official genetic evaluations written in trait-independent format (Format: File300)

• file300Df - daughter deviation file written in trait-independent format

• file300Cr - reduced conventional genetic evaluation file written in trait-independent format

• file300Gr - reduced genomic evaluation file written in trait-independent format

• file736 - file with birth date and genotyping flag (Format: File736)

Running the program

The program should be run from within the programs directory. Typing

python gebvtest.py --help

will give a summary of the program usage:

usage: gebvtest.py [-h] [-v] [-m] [-M MERGEDIR] [-Z] [-C] brd pop datadir

positional arguments:
  brd                   evaluation breed code (BSW/GUE/JER/HOL/RDC/SIM)
  pop                   population code (same as country code except for
                        CHR/DEA/DFS/FRR/FRM)
  datadir               absolute or relative path to data files

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         increase output verbosity
  -m, --mergefiles      write merged data files (for independent data checks)
  -M MERGEDIR, --mergedir MERGEDIR
                        absolute or relative path for merged data files
                        (default=DATADIR/merged)
  -Z, --no-zip          do not create a zip file (eg. for preliminary testing
                        or usage at ITBC)
  -C, --cleanup         delete all files successfully added to the zip file

Output files:

• file735 - results from the GEBV test for all traits tested (Format: File735) (Example)

• gebvtest_log - summary of the calculations (Example)