Services: Cytomapper

cytomapper Service

This script parses either:

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

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": []
}

Links

2020-10-20
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