How to use the bioservices.BioServicesError function in bioservices

To help you get started, we’ve selected a few bioservices examples, based on popular ways it is used in public projects.

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github cokelaer / bioservices / src / bioservices / biomart.py View on Github external
def datasets(self, mart, raw=False):
        """to retrieve datasets available for a mart:

        :param str mart: e.g. ensembl. see :attr:`names` for a list of valid
            MART names the mart is the database. see lookfor method or
            databases attributes

        >>> s = BioMart(verbose=False)
        >>> s.datasets("prod-intermart_1")
        ['protein', 'entry', 'uniparc']

        """
        if mart not in self.names:
            raise BioServicesError("Provided mart name (%s) is not valid. see 'names' attribute" % mart)
        ret = self.http_get("?type=datasets&mart=%s" %mart, frmt="txt")

        if raw is False:
            try:
                ret2 = [x.split("\t") for x in ret.split("\n") if len(x.strip())]
                ret = [x[1] for x in ret2]
            except:
                ret = ["?"]

        return ret
github cokelaer / bioservices / src / bioservices / psicquic.py View on Github external
def show_pie(self):
        """a simple example to demonstrate how to visualise number of
        interactions found in various databases

        """
        try:
            from pylab import pie, clf, title, show, legend
        except ImportError:
            from bioservices import BioServicesError
            raise BioServicesError("You must install pylab/matplotlib to use this functionality")
        labels = range(1, self.N + 1)
        print(labels)
        counting = [len(self.relevant_interactions[i]) for i in labels]

        clf()
        #pie(counting, labels=[str(int(x)) for x in labels], shadow=True)
        pie(counting, labels=[str(x) for x in counting], shadow=True)
        title("Number of interactions found in N databases")
        legend([str(x) + " database(s)" for x in labels])
        show()
github cokelaer / bioservices / src / bioservices / biomart.py View on Github external
def create_filter(self, name, value, dataset=None):
        if dataset:
            valid_filters = self.filters(dataset).keys()
            if name not in valid_filters:
                raise BioServicesError("Invalid filter name. ")
        _filter = ''
        if '=' in value:
            _filter = """        
github cokelaer / bioservices / src / bioservices / biomart.py View on Github external
def create_attribute(self, name, dataset=None):
        #s.attributes(dataset)
        # valid dataset
        if dataset:
            valid_attributes = self.attributes(dataset).keys()
            if name not in valid_attributes:
                raise BioServicesError("Invalid attribute name. ")
        attrib = """        """ % name
        return attrib
github cokelaer / bioservices / src / bioservices / biomart.py View on Github external
def get_xml(self):
        if self.dataset is None:
            raise BioServicesError("data set must be set. Use add_dataset method")
        xml = self.header
        xml += self.dataset + "\n\n"
        for line in self.filters:
            xml += line +"\n"
        for line in self.attributes:
            xml += line + "\n"
        xml += self.footer
        return xml