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genome-nexus / genome-nexus-importer

Import data into MongoDB for use by https://github.com/genome-nexus/genome-nexus/
MIT License
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Mutation assessor v4 #92

Closed leexgh closed 3 months ago

leexgh commented 3 months ago
Part of: https://github.com/genome-nexus/genome-nexus/issues/753 Mutation Assessor v4 data example: uniprotId SV hgvspShort F_score F_impact MSA MAV
P00519 4 p.L25A 3.479676644421987 low P00519.4_full_b0.6_rg0.3 4
P00519 4 p.L25C 4.799205309229616 low P00519.4_full_b0.6_rg0.3 4
P00519 4 p.L25E 0.015792660298301824 neutral P00519.4_full_b0.6_rg0.3 4

We use "uniprotId,hgvspShort" as the index to avoid compound index slowness, the document in mongodb is:

{
  "_id": "P00519,p.L25A",
  "uniprotId": "P00519",
  "sv": 4,
  "hgvspShort": "p.L25A",
  "f_score": 3.479676644421987,
  "f_impact": "low",
  "msa": "P00519.4_full_b0.6_rg0.3",
  "mav": 4
}

Mutation Assessor v4 is available in both grch37 and grch38, version file is updated as well.