GenROC_Public

Public repo for GenROC Project working with Dr Karen Low

HPO Code

All the Python files + notebooks for doing analysis on HPO (Human Phenotype Ontology) related things: https://hpo.jax.org/

HPOFunc.py

A python module for various functions for processing HPO codes.

Main functions of note:

HPOSorter:

• Takes a single cell from the HPOData dataframe
• Checks if it's null
• Then separates it into two separate lists, one list of non_numeric values and one list of numeric values
• The non_numeric values are then cleaned up to remove any leading "HP:" or "hp:" and then returned

HPOOutPutter:

• Takes the two lists from HPOSorter and then runs them through the get_hpo_or_error function
• Numeric values are pretty easy to check
• Non_numeric still require a bit of fiddling
• Also it's quite important to output the errors in a nice way so that they can be manually checked
• This is useful for me to develop this code so that it hits as many common expressions as possible
• But also tells me what I missed.
• It's also just handy because there are some specific entries that are so weird that it's way too much faff to just make a general rule for them. Instead easier to flag and give to my PI who can manually check

HPOSquisher:

• Takes the list of HPO terms from the numeric and non_numeric lists and does the union of them to give a list of all possible mentions
• Sometimes people write stuff in both numeric and non_numeric form, and sometimes just in one or the other process_column:
• Takes the cell entry, runs it through the HPOSorter, HPOOutPutter and HPOSquisher functions
• Returns the terms in a single cell, and any problems that go encountered

HPOScorer:

• Takes a list of HPO terms from the doctor and parent
• returns the quantity and detail scores for both
• as well as the codes where the detail score is non-zero

test_HPOFunc.py

• A python file that loads in HPOFunc.py as a module
• A suite of test functions that assert if the functions in HPOFunc.py give the expected outputs