README for CheckPedigree.py

Updated: 2012-04-28

Information about the program:

CheckPedigree.py will perform a series of checks on your pedigree data to insure that the data is all right. If no errors are detected then a zip file will be created. The zip file represents your checked pedigree file to send to Interbull.

The checks relate to:

Check the international identification numbers (animal, sire and dam)
- Correct three digit country code as in the ISO 3166 standard (no missing countries allowed)
- Correct three digit breed code according to the Interbull breed codes
- Correct construction of the numerical part of the ID (registration numbers, right justified, leading blanks as zeros)
- Missing sires and dams shall be coded as UUUUUUUUUUUUUUUUUUU (i.e. with 19 U)
Check the animal's birth date
- Has to be reported in the format YYYYMMDD
- If you know only the year of birth then enter it as YYYY0000
- If you know year and month of birth then enter them as YYYYMM00
- Missing birth dates are coded as 00000000 (or blanks or a single 0)
Check that a male (or female) animal will eventually appear only as sire (or dam)
Check for inconsistent duplicate records (different sire, dam or birthdate)
Check that an animal is always younger than its parents and grandparents

Before Running the Program:

Install Python (version 2.5 to 2.7) if necessary
Create a working directory/folder
Download the CheckPedigree.py program from https://idea.interbull.org/software and copy it to your new directory
Copy your pedigree file to the working directory

Running the Program:

Ensure there is a working network connection
Use the command: python CheckPedigree.py -m <ORGCODE> -f <filename>
Use your uppercase ORGCODE as shown on the software download page.
The program checks its internal version with the value stored on the Interbull server. You will have to download the most recent version if there is a mismatch.

After Running the Program:

If no errors are detected, the pedigree file will be written into a zip file called IB-ORGCODE-yyyymmddThhmmss.zip. Upload the zip file to Interbull's data exchange site: https://idea.interbull.org/.

In case of errors, no zip file will be created. Please correct your data and re-run the program until the data successfully pass all required checks.

Specific information about your pedigree data, descriptive statistics and a summary of errors are written to the file CheckPedigreeLog.txt.

All errors are listed in detail in the file called CheckPedigreeErrors.txt. The following table describes the brief error messages more fully:

Error message	Description
Inconsistent duplicates	An animal appears twice with different sire, dam or birth date
Warning duplicates	An animal appears twice but with same sire, dam and birth date
Illegal character errors	The numerical part of the international ID is not valid
Breed-country error	The breed-country combination is not recognized - see file CheckPedigreeAuth.txt (created by the program)
Sex coding error	The sex code is neither M nor F
Parent sex error	A male animal (or a female) appears in the dam (or sire) column
Birth date errors	Malformed entry for birth date
Ancestor check	Animal appears older than its parents or grandparents - if a parent's birth date is unknown, grandparents are checked

Note

Please do not modify the program to circumvent any checks. Doing so would be pointless because the same checking routine is used again at the Interbull Centre to double-check the pedigree file uploaded in the zip file.

If you need assistance, please do not hesitate to contact us at interbull-hgen@slu.se .