Differences between revisions 2 and 11 (spanning 9 versions)

Program gebvtest.py - User Manual

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)

-  ⇤ ← Revision 2 as of 2013-01-28 16:35:53 → 
  Size: 2179
  Editor: João
  Comment:
+   ← Revision 11 as of 2013-01-29 17:54:39 → ⇥
  Size: 2913
  Editor: João
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-'''UNDER CONSTRUCTION!'''
-Line 5:
+Line 4:
-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.
  -----------------------------------------------------------------------------
  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
  See detailed instructions at:
  https://wiki.interbull.org/gebvtest_instructions?action=print
  -----------------------------------------------------------------------------
Sample data for program testing
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Some sample data for breed HOL and country 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
The outputs should match those in the source zip file.
+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: [[https://wiki.interbull.org/public/GEBVtest_traits?action=print|traits]])
 * '''''file300Cf''''' - national official genetic evaluations written in trait-independent format (Format: [[https://wiki.interbull.org/public/File300?action=print|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: [[https://wiki.interbull.org/public/File736?action=print|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) ([[https://wiki.interbull.org/public/File735?action=print|Example]])
 * '''''gebvtest_log''''' - summary of the calculations ([[https://wiki.interbull.org/public/gebvtest_log?action=print|Example]])