Map Gene IDs¶

This tutorial will show you how to directly call the GeneWeaver API to map Gene IDs within a species. For this example, we will map Gene Symbols to Ensemble Gene IDs.

To get started, you can

In [1]:

import requests

import requests

Initialize Gene IDs¶

First, you will need to initalize a list of the Gene IDs you want to map. Here, we load identifiers from a file.

After the end of this step you will need to have a list of gene IDs as shown below.

In [2]:

with open('gene_names.txt', 'r') as file:
    file_content = file.read().strip()
    ids = [id.strip('"') for id in file_content.split(',')]

with open('gene_names.txt', 'r') as file: file_content = file.read().strip() ids = [id.strip('"') for id in file_content.split(',')]

In [3]:

len(ids)

len(ids)

Out[3]:

32285

In [4]:

ids[:5]

ids[:5]

Out[4]:

['Xkr4', 'Gm1992', 'Gm19938', 'Gm37381', 'Rp1']

Call The GeneWeaver ReST API¶

First we'll construct our ReST call.

In [5]:

payload = {
    "source_ids": ids,
    "target_gene_id_type": "Ensemble Gene",
    "species": "Mus Musculus"
}

payload = { "source_ids": ids, "target_gene_id_type": "Ensemble Gene", "species": "Mus Musculus" }

The GeneWeaver API uses JSON, so let's specufy that in our request headers.

In [6]:

headers = {
    'accept': 'application/json',
    'Content-Type': 'application/json'
}

headers = { 'accept': 'application/json', 'Content-Type': 'application/json' }

In [7]:

response = requests.post('https://geneweaver.jax.org/api/genes/mapping', json=payload, headers=headers)

response = requests.post('https://geneweaver.jax.org/api/genes/mapping', json=payload, headers=headers)

Process Results¶

The mapping endpoint will return a dictionary with a list of results available on the gene_ids_map key. Let's process that into a dictionary with the original IDs as keys and te new IDs as values.

In [8]:

mapping = {
    r["original_ref_id"]: r["mapped_ref_id"]
    for r in response.json()['gene_ids_map']
}

mapping = { r["original_ref_id"]: r["mapped_ref_id"] for r in response.json()['gene_ids_map'] }

We can now easily access a list of our mapped IDs.

In [9]:

mapped_ids = list(mapping.values())

mapped_ids = list(mapping.values())

In [10]:

len(mapped_ids)

len(mapped_ids)

Out[10]:

32050

In [11]:

mapped_ids[:5]

mapped_ids[:5]

Out[11]:

['ENSMUSG00000066586',
 'ENSMUSG00000027596',
 'ENSMUSG00000030359',
 'ENSMUSG00000027597',
 'ENSMUSG00000019986']

And we can see which IDs couldn't be mapped.

In [12]:

unmapped_ids = [
    _id for _id in ids if _id not in mapping
]

unmapped_ids = [ _id for _id in ids if _id not in mapping ]

In [13]:

len(unmapped_ids)

len(unmapped_ids)

Out[13]:

235

In [14]:

unmapped_ids[:5]

unmapped_ids[:5]

Out[14]:

['Gm28653', 'Ptp4a1.1', 'Arhgef4.1', 'Asdurf', 'AC169382.1']