coderabbitai[bot]
commented
2 months ago Walkthrough
The recent changes significantly enhance the proteomics data analysis codebase, introducing new functionality for polygenic risk score calculations and improved data handling through streaming. Comprehensive documentation and logging capabilities have been added, promoting clarity and monitoring. Additionally, the structure of data classes has evolved to better manage covariates, ensuring robustness and accuracy in genetic data processing.
Changes
| Files | Change Summary |
|---|---|
python/python/bystro/examples/...Query.ipynb |
Updates to execution counts, introduction of streaming functionality, added user credentials, and identified a variable initialization bug. |
python/python/bystro/prs/handler.py, python/python/bystro/prs/messages.py, python/python/bystro/prs/prs_types.py |
Enhanced calculate_prs_scores function with new parameters, and expanded PRSJobData attributes to improve genetic data processing. |
python/python/bystro/prs/listener.py |
Added logging functionality for improved tracking of PRS job operations. |
python/python/bystro/prs/preprocess_for_prs.py |
Refactored code for clarity, added documentation, introduced constants for data handling, and improved PRS calculation logic. |
python/python/bystro/utils/covariates.py |
New file defining structured data classes for covariates and experiment mappings to enhance data integrity and management. |
Sequence Diagram(s)
sequenceDiagram
participant User
participant API
participant PRSHandler
participant PRSJobData
participant Logger
User->>API: Initiate PRS Job
API->>PRSHandler: Call calculate_prs_scores()
PRSHandler->>PRSJobData: Extract parameters
PRSJobData->>PRSHandler: Return parameter data
PRSHandler->>Logger: Log job initiation
PRSHandler->>PRSHandler: Process data
PRSHandler->>Logger: Log processing details
PRSHandler->>API: Return results
User->>API: Receive PRS results🐇 In the fields where we hop and play,
New features bloom, bright as day.
Data streaming flows like a stream,
Together we build, we share a dream.
With logs to guide us, we leap and bound,
In coding joy, our hearts are found! 🌼
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I've attached dave's output vs what I believe is ours. I will double check by re-running again, but this is roughly the difference I recall. Our PRS values are within 10% of Dave's at most, and the differences could be down to precision potentially. I spent a good deal of time tracking down the differences, and it seemed they likely happened in the final step, when adjusting dosages (the ancestry-adjusted allele frequencies were identical, as were the genotypes). I will look into this more in the future, but this PR is a strict improvement, and likely right.
Archive 2.zip
Summary by CodeRabbit
New Features
Bug Fixes
Documentation