Could someone kindly provide an example of using Mutalyzer3 API with Python?

[xiucz]

Could someone kindly provide an example of using Mutalyzer3 API with Python?

[jfjlaros]

I usually use the normalizer in combination with some non-standard and not very well documented syntax that uses the build name as a reference ID, e.g., GRCh38(NM_003002.4):c.92del.

Please note that both the position converter as well as the normalizer (using this syntax) convert between the g. and c. descriptions using the transcript information as annotated on the same reference reference. E.g., it converts between NC_000011.10(NM_003002.4) and NC_000011.10, not between NM_003002.4 and NC_000011.10. The mapper can be used to convert between different reference sequences.

[jfjlaros]

The position_convert method can only be called using a GET request, please see the documentation for more information.

Below is a working example.

import requests


params = {
    'reference_id': 'NC_000011.10',
    'from_selector_id': 'NM_003002.4',
    'from_coordinate_system': 'c',
    'position': '92',
    'to_coordinate_system': 'g',
    'include_overlapping': 'false'}

url = 'https://mutalyzer.nl/api/position_convert'

response = requests.get(url, params=params)
print(response.text)

Output:

{
  "input_model": {
    "reference": {
      "id": "NC_000011.10",
      "selector": {
        "id": "NM_003002.4"
      }
    },
    "coordinate_system": "c",
    "variants": [
      {
        "location": {
          "type": "point",
          "position": 92
        }
      }
    ]
  },
  "converted_model": {
    "reference": {
      "id": "NC_000011.10"
    },
    "coordinate_system": "g",
    "variants": [
      {
        "location": {
          "type": "point",
          "position": 112087896
        }
      }
    ]
  }
}

[xiucz]

Thank you very much for the example. It has helped me to get started with using the API in Python. ^_^. I have been searching for information on how to use the Mutalyzer API for quite some time.

Furthermore, often there is no reference_id information available. Where do you directly obtain the corresponding NC_ information for NM_?

Best,
xiucz

[xiucz]

Thank you for your reminder of the reference version(hg19 or hg38), it is highly appreciated. Mutalyzer2 would indeed be more user-friendly.

[xiucz]

#89 (comment)

I just realized that this is the coordinate system of hg38(default). How can I obtain the results in hg19? Which parameter should I use?

[jfjlaros]

Mutalyzer2 would indeed be more user-friendly.

In what way? The examples above are using version 3.

I just realized that this is the coordinate system of hg38(default).

The position converter does not use any genome build. NC_000011.10 is part of the GRCh37 (hg19) genome build.

[xiucz]

I understand now that GRCh38(NM_003002.4)corresponds to NC_000011.10,

whereas GRCh37(NM_003002.4) corresponds to NC_000011.9.

Thanks a lot!

[jfjlaros]

You are welcome.