Hereditary Tree

Overview

This directory serves as a project for UBIC's Workshop Series, WI24. Currently there are 2 levels of difficulty to the hereditary tree project: one of beginner and one of intermediate difficulty. Each difficulty can be found in the corresponding directory.

Getting Started

1. Make sure you have Python installed. Mac users have python pre-installed, for Windows and Linux go to official Python website. We recommend following some YouTube video on how to install Python, to ensure that everything goes right! To check that Python is installed run this in the terminal:

• Windows & Linux:

  python --version
  

• Mac:

  python3 --version
  

2. Install VS Studio Code if you haven't done so yet. Here's a great intro tutorial to VS Studio Code https://youtu.be/ORrELERGIHs?si=i1y8RGEpFSftlJi7

3. Install Github Desktop. Here is a beginner friendly tutorial: https://youtu.be/8Dd7KRpKeaE?si=VMxvgYu_c-XXqgjT

4. Get started with the project by forking this repository to create your own GitHub repository. Don't forget to invite collaborators, your teammates, in repo's settings (repo – short for repository).

5. When working on beginner/intermediate steps of the project, don't forget to switch into the right folder when running code. In the example below, pay attention that I'm in intermediate folder:

   stephengolzari@Stephens-MacBook-Pro intermediate % python3 heredity_intermediate.py ./data/family1.csv   

   To change directory use ./cd/{directory-name} in the terminal

Now let's go through the details of the project!

Project Details

The whole project can be summed up by the following sentence: given a hereditary tree of the family and information about mutated trait for some members of the family, return probability of each person in the family having the trait.

Command Line

python heredity.py data.csv

• data.csv: Input file in CSV format containing the family tree information. The file should have columns for "name," "mother," "father," and "trait."

Input File Format

The input CSV file should have the following columns:

• name: The name of the individual.
• mother: The name of the mother (or leave it blank if unknown).
• father: The name of the father (or leave it blank if unknown).
• trait: The trait information, represented as 0 (absence of trait), 1 (presence of trait), or blank (unknown trait).

Functionality

1. Probability Calculation:

   • The script calculates the probabilities of each individual having the specified trait based on the trait information of their parents.
   • It considers the genetic inheritance probabilities through the family tree.

2. Output:

   • The script outputs the probabilities for each individual, showing the likelihood of having the trait and the genetic makeup.

3. Handling Unknown Traits: - intermediate level

   • When an individual's trait is unknown, the script should explore the family tree to infer probabilities based on the traits of the known relatives.

Customization

The script uses command-line arguments and allows users to customize the input file and functionality. The arg_parser function defines the command-line arguments, and the script can be modified for additional customization.

Example

Consider the following family tree in data.csv:

name,mother,father,trait
Arthur,,,1
Molly,,,0
Jane,,,1
Tiffany,,,0
Charlie,Molly,Arthur,
Fred,Molly,Arthur,
Sarah,Jane,Charlie,
Ritvik,Tiffany,Fred
Wonka,Sarah,Ritvik

Running the script (here example for intermediate solution on family1.csv dataset):

python heredity_intermediate.py ./data/family1.csv

The output might look like:

Arthur:
  Gene:
    2: 1.0000
    1: 0.0000
    0: 0.0000
  Trait: 1.0
Molly:
  Gene:
    2: 0.0000
    1: 0.0000
    0: 1.0000
  Trait: 0.0
Jane:
  Gene:
    2: 1.0000
    1: 0.0000
    0: 0.0000
  Trait: 1.0
Tiffany:
  Gene:
    2: 0.0000
    1: 0.0000
    0: 1.0000
  Trait: 0.0
Charlie:
  Gene:
    2: 0.0000
    1: 1.0000
    0: 0.0000
  Trait: 0.0
Fred:
  Gene:
    2: 0.0000
    1: 1.0000
    0: 0.0000
  Trait: 0.0
Sarah:
  Gene:
    2: 0.5000
    1: 0.5000
    0: 0.0000
  Trait: 0.5
Ritvik:
  Gene:
    2: 0.0000
    1: 0.5000
    0: 0.5000
  Trait: 0.0
Wonka:
  Gene:
    2: 0.1875
    1: 0.6250
    0: 0.1875
  Trait: 0.1875

Error Handling

The script includes error handling for incorrect command-line usage and checks for the correct file extension.

Note

This README serves as documentation for the usage and functionality of the heredity.py script. Users can refer to this information to understand how to use and customize the script for their specific needs.

This script is part of a broader computational genetics project and serves as a foundation for understanding the probabilities associated with genetic inheritance and traits.

Feel free to explore and modify the script to suit your specific genetic data and research requirements.