Diff for "public/gebvtest_py" - Interbull Centre Wiki

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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.

Input files:

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 dates (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

More detail on the -m --mergefiles options is available here.

Output files

file735 - results from the GEBV test for all traits tested (Format: File735) (Example)
gebvtest_log - summary of the calculations (Example)
Submission zip file - gebvtest.py generates a zip file including all input and output files which should be sent to the Interbull Centre as the official data submission for the GEBV test. The zip file will be named gtYYMM_POPBRD.zip, where YY and MM are year and month of test date, POP is the population code and BRD is the breed code.

-  ⇤ ← Revision 3 as of 2013-01-28 16:40:22 → 
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  Editor: João
  Comment:
+   ← Revision 19 as of 2015-03-10 22:44:09 → ⇥
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  Editor: nilforo
  Comment:
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-= Program gebvtest.py - User Manual =
'''UNDER CONSTRUCTION!'''

=== Information about the program: ===
+== Program gebvtest.py - User Manual ==
=== Information about the program ===
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- .
+=== Input files: ===
 * '''''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 dates (Format: [[https://wiki.interbull.org/public/File736?action=print|File736]])
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-----------
 . 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)
+=== 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)
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+Line 28:
- 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)
+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)
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+Line 37:
-   . or usage at ITBC)
+                        or usage at ITBC)
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+Line 39:
- See detailed instructions at:
 https://wiki.interbull.org/gebvtest_instructions?action=print
+}}}
More detail on the ''-m --mergefiles'' options is available [[https://wiki.interbull.org/public/gebvtest_mergefiles?action=print|here]].
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+Line 42:
-----------
== 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.
+=== Output files ===
 * '''''file735''''' - results from the GEBV test for all traits tested ([[https://wiki.interbull.org/public/File735format?action=print|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]])
 * '''''Submission zip file''''' - gebvtest.py generates a zip file including all input and output files which '''should be sent to the Interbull Centre as the official data submission for the GEBV test'''. The zip file will be named '''''gtYYMM_POPBRD.zip''''', where YY and MM are year and month of test date, POP is the population code and BRD is the breed code.