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README for CheckPedigree.py

Updated: 2012-11-14

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 upload to the Interbull Centre IDEA database.

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:

1. Install Python (version 2.5 to 2.7) if necessary

2. Create a working directory/folder

3. Download the CheckPedigree.py program from https://idea.interbull.org/software and copy it to your new directory

4. 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 upper right hand side of the IDEA page.Your organization code is reported within brackets beside the "Logged in as" information.

• 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:

Note

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

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