test_motifs_api.py

import requests
import json

# MUTAGENE_URL = "https://www.ncbi.nlm.nih.gov/research/mutagene"
# MUTAGENE_URL = "https://dev.ncbi.nlm.nih.gov/research/mutagene"
MUTAGENE_URL = "https://mwebdev2/research/mutagene"
# MUTAGENE_URL = "http://localhost:5000"


def get_motifs(fname, assembly=37):
    """
    Identify mutational motifs in a VCF or MAF sample
    """
    url = MUTAGENE_URL + '/pub/api/identify/motifs'
    files = {'file': open(fname, 'rb')}
    r = requests.post(url, files=files, data={'assembly': assembly})
    if r.status_code == 200:
        return r.json()['motifs']


def print_motifs(motifs):
    """
    Printing the results of motif identification
    """
    if motifs is None:
        print("Empty")
        return
    for m in motifs:
        print("{}\t{}\t{:.2f}\t{:.2e}\t{}".format(
            m['name'], m['motif'],
            m['enrichment'], m['pvalue'],
            m['mutations']))
    print()


if __name__ == '__main__':
    vcf_files = ['test.vcf', ]
    for file_name in vcf_files:
        motifs = get_motifs(file_name, assembly=37)
        print_motifs(motifs)