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How to use create_traceback method in Slash

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MOLITOR_MOROFF_nussinov_predictor.py

Source:MOLITOR_MOROFF_nussinov_predictor.py

...103            # Finally, find maximum104            value = max(opt1, opt2, opt3, opt4)105            mat[row][column + row] = value106    return mat107def create_traceback(matrix, row=0, column=0):108    """Generates a traceback of the Nussinov algorithm109    :param list matrix: list of list filled by fill_matrix110    :param int row: Index in which row the traceback currently is111    :param int column: Index in which column the traceback currently is112    :return list alignment: list of tuples of all bonds113    """114    # Initialisations115    alignment = []116    done = False117    # Traceback118    while matrix[row][column] != 0: # As long as there is atleast one more bond <--> value != 0119        if matrix[row][column] == matrix[row][column - 1]: # If the value left to it is the same move there120            column = column - 1121        elif matrix[row][column] == matrix[row + 1][column]: # If the value below is the same move there122            row = row + 1123        # Check for a bond and move diagonally down-left...124        elif matrix[row][column] == matrix[row + 1][column - 1] + score_au or matrix[row][column] == matrix[row + 1][125            column - 1] + score_gc or matrix[row][column] == matrix[row + 1][column - 1] + score_gu:126            alignment.append((row + 1, column + 1)) # ...add bond to alignment list127            row = row + 1128            column = column - 1129        # If there were two sub-structures continue the traceback of these two substructures130        else:131            for k in range(row + 1, column - 1):132                if matrix[row][column] == matrix[row][k] + matrix[k + 1][column] and not done:133                    alignment += create_traceback(matrix, row=row, column=k)134                    alignment += create_traceback(matrix, row=k + 1, column=column)135                    return alignment136    return alignment137def write_file(alignment, file_name, min_l, gc, au, gu, matrix, seq):138    """Write Output file in a .txt-format139    :param list alignment: list of tuples of the coordinates of bonds140    :param string file_name: Original file name141    :param int min_l: minimum number of residues in loop142    :param int gc: value of gc bonds, for unmodified Nussinov set to 1143    :param int au: value of au bonds, for unmodified Nussinov set to 1144    :param int gu: value of gu bonds, for unmodified Nussinov set to 1145    :param list matrix: List of list which is used as a matrix for Nussinov146    :param str seq: Original RNA sequence147    """148    with open("OutPut.txt", 'a') as file:149        dot_bracket = ""150        file.writelines("Filename: {}\n".format(file_name))151        file.writelines("Min-loop: {}\n".format(min_l))152        file.writelines("GC: {}\n".format(gc))153        file.writelines("AU: {}\n".format(au))154        file.writelines("GU: {}\n".format(gu))155        file.writelines("score: {}\n".format(matrix[0][-1]))156        for i in range(0, len(seq)):157            match = False158            for j in alignment:159                if j[0] == i + 1:160                    dot_bracket = dot_bracket + "("161                    file.writelines(str(j[0]) + "\t" + seq[i] + "\t" + str(j[1]) + "\n")162                    match = True163                elif j[1] == i + 1:164                    dot_bracket = dot_bracket + ")"165                    file.writelines(str(j[1]) + "\t" + seq[i] + "\t" + str(j[0]) + "\n")166                    match = True167            if not match:168                file.writelines(str(i + 1) + "\t" + seq[i] + "\t" + "0" + "\n")169                dot_bracket = dot_bracket + "."170        file.writelines(dot_bracket)171def print_matrix(sequences, matrix):172    """Prints matrix into command line173    :param str sequences: Original RNA sequence174    :param list matrix: List of list --> Nussinov matrix175    """176    first_line = ""177    for i in sequences:178        first_line += "\t" + i179    print(first_line)180    for val, i in enumerate(matrix):181        row = sequences[val]182        for j in i:183            row += "\t" + str(j)184        row += "\n"185        print(row)186#Basic main function187if __name__ == '__main__':188    path, min_loop_len, score_gc, score_au, score_gu = read_data_in()189    headers, sequences = read_fasta(path)190    mst = fill_matrix(sequences[0], min_loop_len, score_gc, score_au, score_gu)191    alignment = create_traceback(mst, column=len(sequences[0]) - 1)192    write_file(alignment, path, min_loop_len, score_gc, score_au, score_gu, mst, sequences[0])...

profiler.py

Source:profiler.py

...48                res = '\n'.join(r[0] for r in cursor.fetchall())49            else:50                res = '(cost=0 rows=0 width=0)\n'51            return res52    def create_traceback(self, request, callback, tracebacks, queries):53        if hasattr(callback, 'cls'):54            view_name = str(callback.cls)55        else:56            view_name = str(callback)57        path = request.build_absolute_uri()58        http_method = request.method59        for tb, q in zip(tracebacks, queries):60            q['traceback'] = tb61            explain = self.get_sql_explaination(q['sql'])62            result = sql_expain_re.search(explain.split('\n')[0])63            q['explain'] = explain64            q['explain_cost'] = result.group("cost")65            q['explain_rows'] = result.group("rows")66            q['explain_width'] = result.group("width")67        total_duration = sum(float(q['time']) for q in queries) * 100068        request_data = {69            'view_name': view_name,70            'path': path,71            'http_method': http_method,72            'total_time': total_duration,73            'total_queries': len(queries),74            'paths': json.dumps(sys.path[1:]),75            'queries': queries,76        }77        self.data = request_data78    def process_request(self, request):79        if 'api' in request.path:80            self.prof = cProfile.Profile()81    def process_view(self, request, callback, callback_args, callback_kwargs):82        if 'api' in request.path:83            logger = TracebackLogger()84            self.prof.enable()85            with connection.execute_wrapper(logger):86                response = self.prof.runcall(87                    callback,88                    request,89                    *callback_args,90                    **callback_kwargs91                )92            self.prof.disable()93            queries = connection.queries.copy()94            self.create_traceback(95                request,96                callback,97                logger.tracebacks,98                queries99            )100            return response101    def process_response(self, request, response):102        if 'api' in request.path:103            try:104                self.prof.disable()105                out = StringIO()106                old_stdout = sys.stdout107                sys.stdout = out108                stats = pstats.Stats(self.prof, stream=out)...

errors.py

Source:errors.py

...21class RTError(Error):22    def __init__(self, details, pos_start, pos_end, context):23        super().__init__(":×××©××× ××¦××¨× ×××× ×××××© ×ª××¨×§", details, pos_start, pos_end)24        self.context = context25    def create_traceback(self):26        result = ''27        pos= self.pos_start28        context = self.context29        30        while context:31            result = f'.{context.dis_name} :× .{str(pos.line + 1)} :××¨××©× {pos.file_name} :×¥×××§× ××\n' + result32            pos = context.parent_position33            context = context.parent34        return ':×¢××¨× ××¨××× ×××  ×××× ×××¨×§× ××××¨××\n\n' + result35 36    def __repr__(self):37        res = self.create_traceback()38        res += f'{self.error_title}\n'39        res += f'{self.details}\n'...

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