Exemple #1
0
    def calculate_distances(self, peptides):
        import sys
        print "@@@", sys.getrecursionlimit()
        dd = self.__d2s.getDistance2Self(p2s(peptides), self.__max_res)
        print "derp"
        result = {key: value.values() for key, value in dd.iteritems()}
        # create temporary file with peptides for distance computation

        resultDf = Distance2SelfResult.from_dict(result)
        resultDf['matrix'] = self.__matrix.name

        return resultDf
Exemple #2
0
    def parse_external_result(self, result):

        """

        :rtype : DataFrame
        """
        parsedResult = {}

        for line in result.strip().split('\n'):
            splitted = line.strip().split(" ")[-1].split(";")
            distanceValues = []
            peptide = splitted[0].split(":")[0]

            for s in splitted[:-1]:
                distanceValues.append(float(s.split(",")[-1]))

            parsedResult[peptide] = distanceValues

        resultDf = Distance2SelfResult.from_dict(parsedResult)
        resultDf['trie'] = self.__trie.split('/')[-1]
        resultDf['matrix'] = self.__matrix.path_to_matrix_file.split('/')[-1]

        return resultDf