Phenofhy

Processing pipeline ​

A typical Phenofhy workflow follows these steps.

For local development, the same downstream processing and summary steps can be tested on simulated data generated with phenofhy.simulate.simulate_phenotype_df().

1) Choose phenotypes ​

Define a list of fields as entity.field strings or via a phenotype list file (which can be referenced in config.json using its file ID).

2) Extract raw data ​

Use extract.fields() to pull data (or generate SQL) from DNAnexus datasets.

For local tests, replace this extraction step with a simulated dataframe.

3) Process by entity ​

Use entity-specific helpers to clean and derive fields:

  • process.participant_fields()
  • process.questionnaire_fields()
  • process.clinic_measurements_fields()

4) Summarize ​

Use calculate.summary() or calculate.prevalence() to create tables for QC or reporting.

5) Profile ​

Use profile.phenotype_profile() to produce a lightweight pre-GWAS phenotype report.

6) Upload ​

Use utils.upload_files() to upload any reports, figures, or tables to your TRE project.

For local testing, this upload step is optional.