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How to use data_as_string method in localstack

Best Python code snippet using localstack_python

ex8.py

Source:ex8.py

1"""2Author: Vali Mikayilov3Matr.Nr.: K120370834Exercise 85"""67import numpy as np8import pandas as pd9import sys1011def count_bases_and_subsequence(data_as_string, subsequence):1213    # We can convert the subsequence string to lower case letters to make the14    # subsequence count case insensitive:15    subsequence = subsequence.lower()  # this converts everything to lower case1617    # We could also convert data_as_string to lower case but this is less18    # memory efficient (we would duplicate the whole string in memory), so we19    # will use a different approach later.2021    # Split file content string into lines22    lines = data_as_string.split("\n")  # alternative: data_as_string.splitlines()2324    # Dictionary to store the counts of individual bases in25    counts = dict(a=0, c=0, g=0, t=0)2627    # Our counter for the subsequence28    subsequence_count = 02930    # Split the subsequence string to a list where each element is a character31    subsequence_list = list(subsequence)3233    # Create a dummy-list which we will later fill with the most recent bases34    # to compare with subsequence_list. We will use None to initialize the35    # list elements. Later we will add None as element instead of a base if36    # the line is invalid.37    recent_bases_list = [None] * len(subsequence_list)3839    # Iterate over all lines40    for line in lines:41        if line == "% End of data":  # End of data reached?42            # If end of data is reached, escape from loop43            break44        elif (len(line) == 0) or line.startswith('%'):  # Invalid data line?45            # Add None to the end and remove first element for subsequence46            # comparison:47            recent_bases_list = recent_bases_list[1:] + [None]48            # If empty line or comment line, skip to next line49            continue5051        # Get values of columns in this line:52        info, base, quality = line.split(";")5354        if float(quality) < 0.08:  # Quality too low?55            # Add None to the end and remove first element for subsequence56            # comparison:57            recent_bases_list = recent_bases_list[1:] + [None]58            # If quality < 0.05, skip to next line59            continue6061        # Remove leading and trailing whitespace characters, just in case62        base = base.strip()6364        # Make sure we are case insensitive65        base = base.lower()6667        # We could use if-elif-else conditions here to increase count-variables68        # for the individual bases. But since we use a dictionary for the69        # counts, we can just use the base itself as key:70        try:71            # Increase counter for the specific base72            counts[base] += 173            # Add the base to the end and remove first element74            recent_bases_list = recent_bases_list[1:] + [base]75        except KeyError:  # Current Base does not exist in our dictionary keys76            # Add None to the end and remove first element for subsequence77            recent_bases_list = recent_bases_list[1:] + [None]78            # If the base entry was not in our dictionary keys, go to the next line79            continue8081        # If the recent bases match the subsequence, we increase the82        # subsequence count by 1:83        if recent_bases_list == subsequence_list:84            subsequence_count += 185            # Add None as last list character to avoid over-lapping matches86            # (this is not relevant for the grading but makes more sense in87            # this setting)88            recent_bases_list = recent_bases_list[1:] + [None]8990    # Return the counts91    return [subsequence_count, counts["a"],counts["c"],counts["g"],counts["t"]]92#ex5.py end93import glob94import os9596def get_hamsters(folderpath):97    found_files = glob.glob(os.path.join(folderpath, '**', '*.raw.seq'), recursive=True)98    found_files = sorted(found_files)99    for x in found_files:100        with open(x, 'r') as f:101            file_content = f.read()102            filename = os.path.basename(x)103            yield filename, file_content104#ex6.py end105import re106matches = ["% SeqHeadStart", "% SeqHeadEnd", "% End of data"]107matches_rest = ['ID:', 'Date:','Columns:']108def  get_file_metadata(data_as_string):109    split_data = data_as_string.split('\n')110    enum_data = enumerate(split_data,0)111    #set the value of the % SeqHeadEnd to a and % End of data to b112    for x in enum_data:113        if x[1] == '% SeqHeadStart':114            a = x[0]115        if x[1] == '% SeqHeadEnd':116            b = x[0]117        if x[1] == '% End of data':118            c = x[0]119    #if the value has all the matches and End of data doesn't come after SeqHead then return an error120    if not all(x in data_as_string for x in matches):121        raise AttributeError(f"the data doesn't contain % SeqHeadStart, % SeqHeadEnd, % End of data")122    if c<b:123        raise AttributeError(f" the End of data doesn't come after SeqHead")124    if b<a:125        raise AttributeError(f" the SeqEnd doesn't come after SeqHead")126    header_slice = slice(0,b+1)127    header = split_data[header_slice]128    # raise attribute error if matches are not found129    if not all(x in data_as_string for x in matches_rest):130        raise AttributeError(f"AttributeError")131    #ID, date and column name132    id = re.findall(r'ID: (\S+)', data_as_string)[0]133    #raise error if the date is incorrect134    try:135        date = int(re.findall(r'Date: (\d+)', data_as_string)[0])136    except (IndexError) as ex:137        raise TypeError(f"TypeError this one")138    else:139        date = int(re.findall(r'Date: (\d+)', data_as_string)[0])140    columns = re.findall(r'Columns: (\S+)', data_as_string)[0]141    columns_split = columns.split(';')142143    for x in header:144        if not x.startswith('%') and not x == '':145            raise AttributeError(f"AttributeError")146    return [id,date]147148x=0149command_line_args = sys.argv150input_folder = command_line_args[1]151output_file = command_line_args[2]152subsequence = command_line_args[3]153file_reader = get_hamsters(input_folder)154arr = np.zeros(shape=(200, 5), dtype=np.float)155f = open(output_file, "a")156for filename, file_content in file_reader:157        data_as_string = file_content158        meta_data = get_file_metadata(data_as_string)159        i = meta_data[1]160        base_count = count_bases_and_subsequence(data_as_string,subsequence)161        arr[i][0] = arr[i][0] + float((base_count[0])/20)162        arr[i][1] = arr[i][1] + float((base_count[1])/20)163        arr[i][2] = arr[i][2] + float((base_count[2])/20)164        arr[i][3] = arr[i][3] + float((base_count[3])/20)165        arr[i][4] = arr[i][4] + float((base_count[4])/20)166
...

ex7.py

Source:ex7.py

1"""2Author: Vali Mikayilov3Matr.Nr.: K120370834Exercise 75"""6import re78matches = ["% SeqHeadStart", "% SeqHeadEnd", "% End of data"]9matches_rest = ['ID:', 'Date:','Columns:']10def  get_file_metadata(data_as_string):11    split_data = data_as_string.split('\n')12    enum_data = enumerate(split_data,0)13    #set the value of the % SeqHeadEnd to a and % End of data to b14    for x in enum_data:15        if x[1] == '% SeqHeadStart':16            a = x[0]17        if x[1] == '% SeqHeadEnd':18            b = x[0]19        if x[1] == '% End of data':20            c = x[0]21    #if the value has all the matches and End of data doesn't come after SeqHead then return an error22    if not all(x in data_as_string for x in matches):23        raise AttributeError(f"the data doesn't contain % SeqHeadStart, % SeqHeadEnd, % End of data")24    if c<b:25        raise AttributeError(f" the End of data doesn't come after SeqHead")26    if b<a:27        raise AttributeError(f" the SeqEnd doesn't come after SeqHead")28    header_slice = slice(0,b+1)29    header = split_data[header_slice]30    # raise attribute error if matches are not found31    if not all(x in data_as_string for x in matches_rest):32        raise AttributeError(f"AttributeError")33    #ID, date and column name34    id = re.findall(r'ID: (\S+)', data_as_string)[0]35    #raise error if the date is incorrect36    try:37        date = int(re.findall(r'Date: (\d+)', data_as_string)[0])38    except (IndexError) as ex:39        raise TypeError(f"TypeError this one")40    else:41        date = int(re.findall(r'Date: (\d+)', data_as_string)[0])42    columns = re.findall(r'Columns: (\S+)', data_as_string)[0]43    columns_split = columns.split(';')4445    for x in header:46        if not x.startswith('%') and not x == '':47            raise AttributeError(f"AttributeError")
...

tcp_control_mode.py

Source:tcp_control_mode.py

1import socket2import _thread3from venv.Experiment.constants import *4from venv.Experiment.arm_movement_control import ArmMotorControl5class TcpControlMode:6    def __init__(self):7        self.serversock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)8        self.serversock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)9        self.serversock.bind(ADDRESS)10        self.serversock.listen(5)11        self.arm = ArmMotorControl()12    def start(self):13        print('waiting for connection... listening on port', PORT)14        while 1:15            clientsock, address = self.serversock.accept()16            # print('...connected from:', address)17            _thread.start_new_thread(self.handler, (clientsock, address))18    @staticmethod19    def response(key):20        return 'Server response: ' + key21    def handler(self, clientsock, address):22        while 1:23            data_as_byte = clientsock.recv(BUFF)24            if not data_as_byte:25                break26            data_as_string = data_as_byte.decode("utf-8")27            data_as_string = str(data_as_string)28            if data_as_string == "ArmClockWise":29                self.arm.turn_clockwise(MOTOR_NAME)30                print("Clockwise sent")31            elif data_as_string == "ArmCounterClockWise":32                self.arm.turn_counter_clockwise(MOTOR_NAME)33                print("Counter clockwise sent")34            else:35                print(f"Received but not understood: {data_as_string}")36            if "close" == data_as_byte.rstrip():37                print("Closing ...")38                break  # type 'close' on client console to close connection from the server side39        clientsock.close()...

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