Source code for bioservices.seqret

#!/usr/bin/python
# -*- coding: latin-1 -*-
#
#  This file is part of bioservices software
#
#  Copyright (c) 2013-2015 - EBI-EMBL
#  Copyright (c) 2016-2017 - Institut Pasteur
#
#  File author(s): thomas cokelaer
#
#  Distributed under the GPLv3 License.
#  See accompanying file LICENSE.txt or copy at
#      http://www.gnu.org/licenses/gpl-3.0.html
#
#  website: https://github.com/cokelaer/bioservices
#  documentation: http://packages.python.org/bioservices
#
##############################################################################
"""This module provides a class :class:`~Seqret` to access to Seqret WS.


.. topic:: What is Seqret ?

    :URL: http://www.ebi.ac.uk/Tools/services/rest/seqret/
    :Service:
    :Citations: http://www.ncbi.nlm.nih.gov/pubmed/18428689

    .. highlights::

        EMBOSS seqret reads and converts biosequences between a selection of common
        biological sequence formats, including EMBL, GenBank and fasta sequence
        formats.

        Seqret homepage -- Sep 2017


"""
import copy
from bioservices.services import REST


__all__ = ["Seqret"]



[docs]class Seqret(): """Interface to the `Seqret <http://www.ebi.ac.uk/readseq>`_ service :: >>> from bioservices import * >>> s = Seqret() The ReadSeq service was replaced by #the Seqret services (2015). .. versionchanged:: 0.15 """ def __init__(self, verbose=True): """.. rubric:: Constructor :param bool verbose: """ url = "https://www.ebi.ac.uk/Tools/services/rest/emboss_seqret" self.services = REST(name="seqret", url=url, verbose=verbose) self._parameters = None
[docs] def get_parameters(self): """Get a list of the parameter names. :returns: a list of strings giving the names of the parameters. """ parameters = self.services.http_get("parameters", frmt="json") return parameters['parameters']
def _get_parameters(self): if self._parameters: return self._parameters else: res = self.get_parameters() self._parameters = res return self._parameters parameters = property(_get_parameters, doc="Get list of parameter names")
[docs] def get_parameter_details(self, parameterId): """Get details of a specific parameter. :param str parameter: identifier/name of the parameter to fetch details of. :return: a data structure describing the parameter and its values. :: rs = ReadSeq() print(rs.get_parameter_details("stype")) """ if parameterId not in self.parameters: raise ValueError("Invalid parameterId provided(%s). See parameters attribute" % parameterId) request = "parameterdetails/" + parameterId res = self.services.http_get(request, frmt="json") return res
[docs] def run(self, email, title, **kargs): """Submit a job to the service. :param str email: user e-mail address. :param str title: job title. :param params: parameters for the tool as returned by :meth:`get_parameter_details`. :return: string containing the job identifier (jobId). Deprecated (olf readseq service):: Format Name Value Auto-detected 0 EMBL 4 GenBank 2 Fasta(Pearson) 8 Clustal/ALN 22 ACEDB 25 BLAST 20 DNAStrider 6 FlatFeat/FFF 23 GCG 5 GFF 24 IG/Stanford 1 MSF 15 NBRF 3 PAUP/NEXUS 17 Phylip(Phylip4) 12 Phylip3.2 11 PIR/CODATA 14 Plain/Raw 13 SCF 21 XML 19 As output, you also have Pretty 18 :: s = readseq.Seqret() jobid = s.run("cokelaer@test.co.uk", "test", sequence=fasta, inputformat=8, outputformat=2) genbank = s.get_result(s._jobid) """ for k in kargs.keys(): self.services.devtools.check_param_in_list(k, self.parameters) assert "sequence" in kargs.keys() params = {"email":email, "title":title} for k in ['stype', 'inputformat','outputformat', "feature", "firstonly", "reverse", 'outputcase', 'seqrange']: if k in kargs.keys(): value = kargs.get(k) details = self.get_parameter_details(k) valid_values = [x['value'] for x in details['values']['values']] self.services.devtools.check_param_in_list(str(value), valid_values) params[k] = value #r = requests.post(url + "/run?", data={"sequence":fasta, "stype": "protein", #"inputformat":"raw", "outputformat":"fasta", "email":"thomas.cokelaer@pasteur.fr", #"title":"test"}) params['sequence'] = kargs['sequence'] jobid = self.services.http_post("run", frmt="txt", data=params) self._jobid = jobid return jobid
[docs] def get_status(self, jobid=None): """Get the status of a submitted job. :param str jobid: job identifier. :return: string containing the status. The values for the status are: - RUNNING: the job is currently being processed. - FINISHED: job has finished, and the results can then be retrieved. - ERROR: an error occurred attempting to get the job status. - FAILURE: the job failed. - NOT_FOUND: the job cannot be found. """ res = self.services.http_get("status/{}".format(jobid), frmt="txt") return res
[docs] def get_result_types(self, jobid): """Get the available result types for a finished job. :param str jobid: job identifier. :return: a list of wsResultType data structures describing the available result types. """ res = self.services.http_get("resulttypes/{}".format(jobid), frmt="json") return [x['identifier'] for x in res["types"]]
[docs] def get_result(self, jobid, result_type="out"): """Get the result of a job of the specified type. :param str jobid: job identifier. :param parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types. """ if self.get_status(jobid) != 'FINISHED': self.services.logging.warning("Your job is not finished yet. Try again later.") return #result_types = self.get_result_types(jobid) #assert parameters in result_types res = self.services.http_get("result/{}/{}".format(jobid, result_type), frmt="txt") return res