2 results found

1. Boost the performance of bioinformatic annotation queries

   The documents to be selected look something like this:

   {
   "_id": {
   "$oid": "6272c580d4400d8cb10d5406"
   },
   "#CHROM": 1,
   "POS": 286747,
   "ID": "rs369556846",
   "REF": "A",
   "ALT": "G",
   "QUAL": ".",
   "FILTER": ".",
   "INFO": [{
   "RS": 369556846,
   "RSPOS": 286747,
   "dbSNPBuildID": 138,
   "SSR": 0,
   "SAO": 0,
   "VP": "0x050100000005150026000100",
   "WGT": 1,
   "VC": "SNV",
   "CAF": [{
   "$numberDecimal": "0.9381"
   }, {
   "$numberDecimal": "0.0619"
   }],
   "COMMON": 1,
   "TOPMED": [{
   "$numberDecimal": "0.88411856523955147"
   }, {
   "$numberDecimal": "0.11588143476044852"
   }]
   },
   ["SLO", "ASP", "VLD", "G5", "KGPhase3"]
   ]
   }

   For a basic annotation (https://en.wikipedia.org/wiki/SNP_annotation) scenario, we need such query:

   {'ID': {'$in': ['rs369556846', 'rs2185539', 'rs2519062', 'rs149363311', 'rs55745762', <...>]}}
   , where <...> means hundreds/thousands of values.

   Such query is executed in a few seconds.

   More complex annotation queries:

   {'$or': [{'#CHROM': 1, 'POS': 1499125}, {'#CHROM': 1, 'POS': 1680158}, {'#CHROM': 1, 'POS': 1749174}, {'#CHROM': 1, 'POS': 3061224}, {'#CHROM': 1, 'POS': 3589337}, <...>]}

   {'$or': [{'ID': 'rs149434212', 'REF': 'C', 'ALT': 'T'}, {'ID': 'rs72901712', 'REF': 'G', 'ALT': 'A'}, {'ID': 'rs145474533', 'REF': 'G', 'ALT': 'C'}, {'ID': 'rs12096573', 'REF': 'G', 'ALT': 'T'}, {'ID': 'rs10909978', 'REF': 'G', 'ALT': 'A'}, <...>]}

   Despite the involvement of IXSCAN, they run many hours.

   Please test aforementioned queries thoroughly and improve the performance of their execution. This will help science!

   The documents to be selected look something like this:

   {
   "_id": {
   "$oid": "6272c580d4400d8cb10d5406"
   },
   "#CHROM": 1,
   "POS": 286747,
   "ID": "rs369556846",
   "REF": "A",
   "ALT": "G",
   "QUAL": ".",
   "FILTER": ".",
   "INFO": [{
   "RS": 369556846,
   "RSPOS": 286747,
   "dbSNPBuildID": 138,
   "SSR": 0,
   "SAO": 0,
   "VP": "0x050100000005150026000100",
   "WGT": 1,
   "VC": "SNV",
   "CAF": [{
   "$numberDecimal": "0.9381"
   }, {
   "$numberDecimal": "0.0619"
   }],
   "COMMON": 1,
   "TOPMED": [{
   "$numberDecimal": "0.88411856523955147"
   }, {
   "$numberDecimal": "0.11588143476044852"
   }]
   },
   ["SLO", "ASP", "VLD", "G5", "KGPhase3"]
   ]
   }

   For a basic annotation (https://en.wikipedia.org/wiki/SNP_annotation) scenario, we need such query:

   {'ID': {'$in': ['rs369556846', 'rs2185539', 'rs2519062', 'rs149363311', 'rs55745762', <...>]}}
   , where <...> means hundreds/thousands… more

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2. There is a specific collection that I need more performance than others. Is there a way to assign more ram/memory to a specific collection?

   There is a specific collection that I need more performance than others. Is there a way to assign more ram/memory to a specific collection?

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   0 comments  ·  Performance  ·  Flag idea as inappropriate…Flag idea as inappropriate…  ·  Edit…  ·  Delete…  ·  Admin →
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