CohortEncoder

This class coordinates the extract-transform-load (ETL) operations for a cohort, usually taken from a table in a publication or supplemental file. It is intended to be used with the ColumnMappers to map each relevant column of the table.

CohortEncoder constructor

pmid = "PMID:30612693"
encoder = CohortEncoder(df=dft, hpo_cr=hpo_cr, column_mapper_d=column_mapper_d, 
                      individual_column_name="patient_id", 
                      agemapper=ageMapper, 
                      sexmapper=sexMapper,
                      metadata=metadata,
                      variant_mapper=varMapper,
                      pmid=pmid)
disease_id = "OMIM:618443"
disease_label = "Neurodevelopmental disorder with or without variable brain abnormalities"
encoder.set_disease(Disease(disease_id=disease_id, disease_label=disease_label))

Display a phenopacket

Optionally, it can be useful to displayand manually assess a phenopackets

Display a phenopacket

individuals = encoder.get_individuals()
i1 = individuals[0]
phenopacket1 = i1.to_ga4gh_phenopacket(metadata=metadata.to_ga4gh())
json_string = MessageToJson(phenopacket1)
print(json_string)