motif-broker-request 1.0.0

Package to interrogate motif-broker JS microservice with python

motif-broker-request

Example in test/test.py

Configure motif-broker-request

import motif_broker_request.request as mb_request

mb_request.configure("http://localhost:5984") #Default is localhost:3282

You can also change bulk length

mb_request.set_bulk_length(10000) #Default is 50000

Request motif-broker

sgrnas = ["AAAAAAAAAAAAAAAAAAATGGG", "TCCAAAAAAAAACAGTGGATTGG", "CACTAAAAAAGAAGACCAAGCGG"] # sgRNAs you want to search
res = mb_request.get(sgrnas)

print(res)

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Request motif-broker with some filter

You can write filter functions. This functions have to take motif_broker results as arguments and return the filtered version with same format

Example of function that just keep given genomes in results :

def filter_genomes(mb_res, **kwargs):
    if not "genomes" in kwargs:
        raise Exception("you must provide 'genomes' argument to get function for filter_genomes function")
    genomes = kwargs["genomes"]

    filtered_results = {}
    for sgrna in mb_res: 
        added = False 
        for org in mb_res[sgrna]:
            if org in genomes:
                if added:
                    filtered_results[sgrna][org] = mb_res[sgrna][org]
                else:
                    filtered_results[sgrna] = {org : mb_res[sgrna][org]}

    return filtered_results

Applied this way to get results :

res = mb_request.get(sgrnas, filter_predicate=filter_genomes, genomes=["dd6cfb980c8a3659acffa4f002ea7404", "dd6cfb980c8a3659acffa4f0029ff84a"])
print(res)

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