This script parses either:
assemblyId
, cytoBands
)
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.
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
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
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": []
}