querying metadata (GDC Data Portal) in python3

Question

I am trying to query metadata from the Genomic Data Commons (GDC) Data Portal and used the sample code from its website:

import requests
import json

cases_endpt = 'https://api.gdc.cancer.gov/cases'

# The 'fields' parameter is passed as a comma-separated string of single names.
fields = ["submitter_id",
          "case_id",
          "primary_site",
          "disease_type",
          "diagnoses.vital_status"
         ]

fields = ','.join(fields)

params = {"fields": fields,
          "format": "TSV",
          "size": "100"
         }

response = requests.get(cases_endpt, params = params)

print(response.content)

However, I am not getting a tsv file in return. I am ultimately getting an FPKM instead. Any help is appreciated!

Answer 1

You can use str() to convert bytes to strings and print() with the proper separator.

import requests
from io import StringIO
import pandas as pd

cases_endpt = 'https://api.gdc.cancer.gov/cases'

fields = ["submitter_id",
          "case_id",
          "primary_site",
          "disease_type",
          "diagnoses.vital_status"
          ]

fields = ','.join(fields)

params = {"fields": fields,
          "format": "TSV",
          "size": "100"
          }

response = requests.get(cases_endpt, params=params)

content = str(response.content, 'utf-8')

print(content, sep='\t', end='\r')

If you want to convert to a data frame you can use StringIO() to load a data frame from an input string directly to a pandas data frame.

data = StringIO(content)
df = pd.read_csv(data, sep='\t')

The output:

	case_id	disease_type	id	primary_site	submitter_id
0	375436b3-66ac-4d5e-b495-18a96d812a69	Adenomas and Adenocarcinomas	375436b3-66ac-4d5e-b495-18a96d812a69	Rectum	TCGA-F5-6810
1	38f93ca8-4971-4932-b592-0a17eaece2ad	Ductal and Lobular Neoplasms	38f93ca8-4971-4932-b592-0a17eaece2ad	Pancreas	C3L-02115
2	5ea1361a-050d-4fa0-be59-b530c456b6e3	Ductal and Lobular Neoplasms	5ea1361a-050d-4fa0-be59-b530c456b6e3	Pancreas	C3L-00928
3	690378f3-e38a-4b25-8489-05a3b4bd40b6	Adenomas and Adenocarcinomas	690378f3-e38a-4b25-8489-05a3b4bd40b6	Kidney	C3N-01175
4	6b4f086e-4ef9-4f30-874e-8a155b2e3bab	Squamous Cell Neoplasms	6b4f086e-4ef9-4f30-874e-8a155b2e3bab	Other and ill-defined sites	C3N-04276