INNER CODE UNIT · Python

mapper

ncbi/dbsnp · tutorials/hadoop_json_placement.py:52

    def mapper(self, _, line):

        data = json.loads(line)

        snp_id = data["refsnp_id"]

        placements = data["primary_snapshot_data"]["placements_with_allele"]

        for p in placements:
            is_ptlp = str(int(p["is_ptlp"] == "true"))
            is_aln_opposite_orientation = str(int(
                p["placement_annot"]["is_aln_opposite_orientation"] == "true"))
            is_mismatch = str(
                int(p["placement_annot"]["is_mismatch"] == "true"))
            for a in p["alleles"]:
                if "spdi" in a["allele"]:
                    spdi = a["allele"]["spdi"]
                    hgvs = a["hgvs"]

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