test_api.py

import requests
import json

MUTAGENE_URL = "https://www.ncbi.nlm.nih.gov/research/mutagene"


def get_profile(fname, assembly=37):
    """
    Calling MutaGene REST API to convert a VCF file into a mutational profile (96 context-dependent mutational probabilities)
    and profile_counts (counts of mutations for each of the 96 context-dependent mutations)
    It is important to specify genome assembly correctly. Curently 19, 37 and 38 will work
    """
    url = MUTAGENE_URL + '/pub/api/identify/profile'
    files = {'file': open(fname, 'rb')}
    r = requests.post(url, files=files, data={'assembly': assembly})
    # print("STATUS", r.status_code)
    if r.status_code == 200:
        return r.json()['result_counts']


def get_decomposition(profile_counts, signatures='COSMIC30'):
    """
    Decomposition of mutational profiles into a combination of signatures.
    It is highly recommended to use profile_counts instead of profile in order to use Maximum Likelihood method

    *signatures* should be one of COSMIC30  MUTAGENE5 MUTAGENE10
    *others_threshold* is used for not reporting signatures with exposure less or equal than the threshold and reporting the sum of their exposures as "Other signatures".
    Set *others_threshold* to 0 if not needed. The MutaGene website uses others_threshold = 0.05 by default.
    """
    url = MUTAGENE_URL + '/pub/api/identify/decomposition'
    r = requests.post(url, data={'profile_counts': json.dumps(profile_counts), 'signatures': signatures, 'others_threshold': 0.0})
    # print("STATUS", r.status_code)
    if r.status_code == 200:
        return r.json()['decomposition']


def print_profile_counts(profile_counts):
    """
    Printing context-dependent mutational profile
    """
    for mutation, value in profile.items():
        print("{}\t{:.0f}".format(mutation, value))
    print()


def print_decomposition(decomposition):
    """
    Printing the results of decomposition
    """
    for component in decomposition:
        print("{}\t{:.2f}\t{:.0f}".format(component['name'], component['score'], component['mutations']))
    print()


if __name__ == '__main__':
    vcf_files = ['test.vcf', ]
    for file_name in vcf_files:
        profile = get_profile(file_name, assembly=37)
        print_profile_counts(profile)

        if profile is not None:
            for signature_type in ('COSMIC30', 'MUTAGENE5', 'MUTAGENE10'):
                decomposition = get_decomposition(profile, signature_type)
                print_decomposition(decomposition)

Test output for my VCF is

            A[C>A]A 119
            A[C>A]C 114
            A[C>A]G 86
            A[C>A]T 64
            A[C>G]A 174
            A[C>G]C 90
            A[C>G]G 123
            A[C>G]T 125
            A[C>T]A 475
            A[C>T]C 372
            A[C>T]G 1423
            A[C>T]T 480
            A[T>A]A 53
            A[T>A]C 74
            A[T>A]G 68
            A[T>A]T 58
            A[T>C]A 466
            A[T>C]C 330
            A[T>C]G 1344
            A[T>C]T 512
            A[T>G]A 69
            A[T>G]C 59
            A[T>G]G 95
            A[T>G]T 67
            C[C>A]A 126
            C[C>A]C 136
            C[C>A]G 157
            C[C>A]T 96
            C[C>G]A 129
            C[C>G]C 147
            C[C>G]G 197
            C[C>G]T 165
            C[C>T]A 372
            C[C>T]C 397
            C[C>T]G 1594
            C[C>T]T 538
            C[T>A]A 25
            C[T>A]C 60
            C[T>A]G 114
            C[T>A]T 81
            C[T>C]A 316
            C[T>C]C 389
            C[T>C]G 1356
            C[T>C]T 542
            C[T>G]A 45
            C[T>G]C 153
            C[T>G]G 170
            C[T>G]T 90
            G[C>A]A 123
            G[C>A]C 110
            G[C>A]G 163
            G[C>A]T 77
            G[C>G]A 145
            G[C>G]C 144
            G[C>G]G 143
            G[C>G]T 129
            G[C>T]A 330
            G[C>T]C 396
            G[C>T]G 1067
            G[C>T]T 481
            G[T>A]A 42
            G[T>A]C 54
            G[T>A]G 81
            G[T>A]T 52
            G[T>C]A 295
            G[T>C]C 359
            G[T>C]G 912
            G[T>C]T 441
            G[T>G]A 67
            G[T>G]C 90
            G[T>G]G 154
            G[T>G]T 84
            T[C>A]A 75
            T[C>A]C 87
            T[C>A]G 48
            T[C>A]T 60
            T[C>G]A 157
            T[C>G]C 137
            T[C>G]G 130
            T[C>G]T 181
            T[C>T]A 290
            T[C>T]C 331
            T[C>T]G 728
            T[C>T]T 399
            T[T>A]A 18
            T[T>A]C 52
            T[T>A]G 28
            T[T>A]T 54
            T[T>C]A 251
            T[T>C]C 332
            T[T>C]G 633
            T[T>C]T 344
            T[T>G]A 60
            T[T>G]C 124
            T[T>G]G 109
            T[T>G]T 88

            COSMIC 1    0.29    7113
            COSMIC 26   0.21    5195
            COSMIC 3    0.18    4526
            COSMIC 20   0.15    3743
            COSMIC 12   0.10    2432
            COSMIC 30   0.06    1591
            COSMIC 24   0.01    265

            MUTAGENE A.3    0.52    12979
            MUTAGENE A.5    0.25    6347
            MUTAGENE A.4    0.11    2621
            MUTAGENE A.1    0.07    1745
            MUTAGENE A.2    0.05    1201

            MUTAGENE B.6    0.35    8676
            MUTAGENE B.1    0.15    3855
            MUTAGENE B.2    0.13    3302
            MUTAGENE B.7    0.11    2836
            MUTAGENE B.9    0.06    1545
            MUTAGENE B.3    0.05    1300
            MUTAGENE B.10   0.05    1206
            MUTAGENE B.4    0.04    985
            MUTAGENE B.5    0.03    863
            MUTAGENE B.8    0.01    328