INNER CODE UNIT · Python

mapper

ncbi/dbsnp · tutorials/hadoop_json_annotation.py:56

    def mapper(self, _, line):

        data = json.loads(line)

        snp_id = data["refsnp_id"]

        annotations = data["primary_snapshot_data"]["allele_annotations"]

        for a in annotations:
            assembly_annotations = a["assembly_annotation"]
            for aa in assembly_annotations:
                seq_id = aa["seq_id"]
                annotation_release = aa["annotation_release"]
                genes = aa["genes"]

                for g in genes:
                    gene_name = g["name"]
                    gene_id = str(g["id"])

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