cathpy.funfhmmer

from cathpy.funfhmmer import Client

api = Client()

response = api.search_fasta(fasta_file='/path/to/seq.fa')

response.as_csv()

CATH FunFHMMER - tool for remote sequence search against CATH FunFams

class cathpy.funfhmmer.ApiClientBase(base_url, *, default_accept='application/json')

Base class implementing default local behaviour of an API client.

get(url, *, accept=None)

Performs a GET request

post(url, *, accept=None)

Performs a POST request

class cathpy.funfhmmer.CheckResponse(*, data, message, success, **kwargs)

Class that represents the response from FunFHMMER STATUS request.

class cathpy.funfhmmer.Client(*, base_url='http://www.cathdb.info', sleep=2, retries=50, log=None)

Client for the CATH FunFhmmer API (protein sequence search server).

The CATH FunFhmmer server allows users to locate matching CATH Functional Families (FunFams) in their protein sequence.

check(task_id)

Checks the status of an existing search.

results(task_id)

Retrieves the results of a search.

search_fasta(fasta=None, fasta_file=None)

Submits a sequence search and retrieves results.

submit(fasta)

Submits a protein sequence to be searched and returns a task_id.

class cathpy.funfhmmer.ResponseBase(**kwargs)

Base class that represents the HTTP response.

class cathpy.funfhmmer.ResultResponse(*, query_fasta, funfam_scan, cath_version, **kwargs)

Class that represents the response from FunFHMMER RESULTS request.

as_csv()

Returns the result as CSV

as_json(*, pp=False)

Returns the response as JSON formatter string.

class cathpy.funfhmmer.SubmitResponse(**kwargs)

Class that represents the response from FunFHMMER SUBMIT request.