inbreeding-calculator 1.0.1

Calculate the inbreeding coefficient of a pedigree in Python.

inbreeding-calculator

Inbreeding Coefficient Calculator for Pedigrees in Python

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Installation

pip install inbreeding-calculator

How to use

1. Create a python dictionary containing a pedigree.

   # Pedigree example with 0.25 inbreeding coefficient (25%)
   pedigree = {
       "sire": {
           "sire": None,
           "dam": None,
           "id": "2834",
       },
       "dam": {
           "sire": {
               "sire": None,
               "dam": None,
               "id": "2834",
           },
           "dam": None,
           "id": "781",
       },
       "id": "622",
   }
   

   All animals in pedigree must have a unique id. If the sire/dam of an animal is unknown the value can be set to None or the key can be omitted all together.

2. Import the InbreedingCalculator.

   from inbreeding_calculator import InbreedingCalculator
   

3. Create an instance of the InbreedingCalculator class and load the pedigree.

   calculator = InbreedingCalculator(pedigree)
   

   or

   calculator = InbreedingCalculator()
   calculator.pedigree = pedigree
   

4. Configure Calculator

   If you used keys other than sire, dam & id ensure you configure your InbreedingCalculator object for them.

   pedigree = {
   "Father": None,
   "Mother": None,
   "Name": "Billy"
   }
   
   calculator = InbreedingCalculator(pedigree, "Father", "Mother", "Name")
   

   or

   calculator = InbreedingCalculator(pedigree)
   calculator.sire_key = "Father"
   calculator.dam_key = "Mother"
   calculator.id_key = "Name"
   

5. Use the get_coefficient method to find the inbreeding percentage

   pedigree = {
       "sire": {
           "sire": None,
           "dam": None,
           "id": "2834",
       },
       "dam": {
           "sire": {
               "sire": None,
               "dam": None,
               "id": "2834",
           },
           "dam": None,
           "id": "781",
       },
       "id": "622",
   }
   
   calculator = InbreedingCalculator(pedigree)
   ic = calculator.get_coefficient()
   print(f"Inbreeding Coefficient: {ic} ({ic * 100}%)")
   

   Output

   Inbreeding Coefficient: 0.25 (25.0%)
   

If you use this code please give proper credit.

Thank you, Owen Dechow!