Services: Cytomapper

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cytomapper Service

This services parses either:

• a properly formatted cytoband annotation (assemblyId, cytoBands)
  • “8”, “9p11q21”, “8q”, “1p12qter”
• a concatenated chroBases parameter
  • 7:23028447-45000000
  • X:99202660

While the return object is JSON by default, specifying text=1, together with the cytoBands or chroBases parameter will return the text version of the opposite.

There is a fallback to GRCh38 if no assembly is being provided.

The cytobands and chrobases parameters can be used for running the script on the command line (see examples below). Please be aware of the “chrobases” (command line) versus “chroBases” (cgi) use.

Examples

• retrieve coordinates for some bands on chromosome 8
  • https://progenetix.org/services/cytomapper?assemblyId=NCBI36.1&cytoBands=8q24.1
• as above, just as text:
  • https://progenetix.org/services/cytomapper?assemblyId=NCBI.1&cytoBands=8q&text=1
  • cytomapper shortcut: https://progenetix.org/services/cytomapper/?assemblyId=NCBI36.1&cytoBands=8q&text=1
• get the cytobands whith which a base range on chromosome 17 overlaps, in short and long form
  • https://progenetix.org/services/cytomapper?assemblyId=GRCh37&chroBases=17:800000-24326000
• using curl to get the text format mapping of a cytoband range, using the API services shortcut:
  • curl -k https://progenetix.org/services/cytomapper?cytoBands\=8q21q24.1&assemblyId\=hg18&text\=1
• command line version of the above
  • bin/cytomapper.py --chrobases 17:800000-24326000 -g NCBI36
  • bin/cytomapper.py -b 17:800000-24326000
  • bin/cytomapper.py --cytobands 9p11q21 -g GRCh38
  • bin/cytomapper.py -c Xpterq24

Response

As in other bycon services, API responses are in JSON format with the main content being contained in the data field.

As of v2020-09-29, the ChromosomeLocation response is compatible to the GA4GH VRS standard. The GenomicLocation object is a wrapper around a VRS SimpleInterval.

{
  "data": {
    "ChromosomeLocation": {
      "chr": "8",
      "interval": {
        "end": "q24.13",
        "start": "q24.11",
        "type": "CytobandInterval"
      },
      "species_id": "taxonomy:9606",
      "type": "ChromosomeLocation"
    },
    "GenomicLocation": {
      "chr": "8",
      "interval": {
        "end": 127300000,
        "start": 117700000,
        "type": "SimpleInterval"
      },
      "species_id": "taxonomy:9606",
      "type": "GenomicLocation"
    },
    "info": {
      "bandList": [
        "8q24.11",
        "8q24.12",
        "8q24.13"
      ],
      "chroBases": "8:117700000-127300000",
      "cytoBands": "8q24.11q24.13",
      "referenceName": "8",
      "size": 9600000
    }
  },
  "errors": [],
  "parameters": {
    "assemblyId": "NCBI36.1",
    "cytoBands": "8q24.1"
  },
  "response_type": "cytomapper",
  "warnings": []
}

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