inbreeding-calculator 1.0.0

Calculate the inbreeding coefficient of a pedigree in Python.

inbreeding-python

Inbreeding Coefficient Calculator for Pedigrees in Python

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

   calculator = InbreedingCalculator(pedigree)
   

   or

   calculator = InbreedingCalculator()
   calculator.pedigree = pedigree
   

3. 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"
   

4. 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!