hl7v2GenomicsExtractor

Introduction

HL7 Version 2 messaging format is the predominant means by which labs send structured results to Electronic Health Records (EHRs). EHRs can directly import HL7 V2 formatted results that conform to the HL7 Lab Results Interface Implementation Guide. Here, we provide an open source utility for converting variants from VCF/XML format into HL7 V2 format.

Install

Before installing hl7v2GenomicsExtractor you need to install cython and wheel.

pip install cython wheel

Now, install hl7v2GenomicsExtractor binary from pip.

pip install hl7v2GenomicsExtractor

>>> import hl7v2GenomicsExtractor
>>> hl7v2GenomicsExtractor_converter = hl7v2GenomicsExtractor.Converter(filename="sample.xml", ref_build="GRCh37", patient_id=1234, seed=1, source_class="somatic", variant_analysis_method="sequencing")
>>> hl7v2GenomicsExtractor_converter.convert()

License and Limitations

Software is available for use under an Apache 2.0 license, and is intended solely for experimental use, to help further Genomics-EHR integration exploration. Software is expressly not ready to be used with identifiable patient data or in delivering care to patients. Code issues should be tracked here.