Update 2023-Spring/2023-02-28-session-04/protein-mw-tk-v2.py,...

'''

This code uses the tkinter library to create file dialogs for selecting the 

input and output files, and the guizero library to create a simple GUI with 

text boxes and buttons. The analyze_protein function reads the protein 

sequence from the input file selected by the user, analyzes its amino acid 

composition using the same code as before, and saves the result in the 

output file selected by the user.

'''

import os

import tkinter as tk

from tkinter import filedialog

from guizero import App, Text, TextBox, PushButton

amino_acids = {'A': 'Alanine', 'C': 'Cysteine', 'D': 'Aspartic Acid', 'E': 

'Glutamic Acid',

               'F': 'Phenylalanine', 'G': 'Glycine', 'H': 'Histidine', 'I': 

'Isoleucine',

               'K': 'Lysine', 'L': 'Leucine', 'M': 'Methionine', 'N': 

'Asparagine',

               'P': 'Proline', 'Q': 'Glutamine', 'R': 'Arginine', 'S': 

'Serine',

               'T': 'Threonine', 'V': 'Valine', 'W': 'Tryptophan', 'Y': 

'Tyrosine'}

def select_input_file():

    root = tk.Tk()

    root.withdraw()

    file_path = filedialog.askopenfilename(filetypes=[("Text files", 

"*.txt")])

    input_file.value = file_path

def select_output_file():

    root = tk.Tk()

    root.withdraw()

    file_path = filedialog.asksaveasfilename(defaultextension=".md")

    output_file.value = file_path

app = App(title="Protein Analysis")

Text(app, text="Select input file:")

input_file = TextBox(app, width=50)

PushButton(app, command=select_input_file, text="Browse...")

Text(app, text="Output file name:")

output_file = TextBox(app, width=50)

PushButton(app, command=select_output_file, text="Browse...")

def analyze_protein():

    with open(input_file.value, "r") as f:

        protein_sequence = f.read().strip()

    aa_count = {}

    for aa in amino_acids:

        aa_count[aa] = protein_sequence.count(aa)

    total_aa = sum(aa_count.values())

    with open(output_file.value, "w") as f:

        f.write("# Protein Composition\n\n")

        f.write("Amino Acid | Count | Percentage\n")

        f.write("--- | --- | ---\n")

        for aa, count in aa_count.items():

            percentage = (count / total_aa) * 100

            f.write(f"{amino_acids[aa]} | {count} | {percentage:.2f}%\n")

PushButton(app, command=analyze_protein, text="Analyze Protein")

app.display()

'''

WARNING:

THIS CODE will not allow you to select the .txt or the .pep file.

It is here to show FAILURE

'''

'''

V1:

This code uses the tkinter library to create file dialogs for selecting the 

input and output files, and the guizero library to create a simple GUI with 

text boxes and buttons. The analyze_protein function reads the protein 

sequence from the input file selected by the user, analyzes its amino acid 

composition using the same code as before, and saves the result in the 

output file selected by the user.

'''

'''

V2: 

This code adds a check for the existence of the input file, and displays an 

error message if it doesn't exist. It also displays a success message with 

the output file name when the analysis is completed and the output file is 

written.

'''

import os

import tkinter as tk

from tkinter import filedialog

from guizero import App, Text, TextBox, PushButton, info

amino_acids = {'A': 'Alanine', 'C': 'Cysteine', 'D': 'Aspartic Acid', 'E': 

'Glutamic Acid',

               'F': 'Phenylalanine', 'G': 'Glycine', 'H': 'Histidine', 'I': 

'Isoleucine',

               'K': 'Lysine', 'L': 'Leucine', 'M': 'Methionine', 'N': 

'Asparagine',

               'P': 'Proline', 'Q': 'Glutamine', 'R': 'Arginine', 'S': 

'Serine',

               'T': 'Threonine', 'V': 'Valine', 'W': 'Tryptophan', 'Y': 

'Tyrosine'}

def select_input_file():

    root = tk.Tk()

    root.withdraw()

    file_path = filedialog.askopenfilename(filetypes=[("Text files", 

"*.txt;*.pep")])

    input_file.value = file_path

def select_output_file():

    root = tk.Tk()

    root.withdraw()

    file_path = filedialog.asksaveasfilename(defaultextension=".md")

    output_file.value = file_path

app = App(title="Protein Analysis")

Text(app, text="Select input file:")

input_file = TextBox(app, width=50)

PushButton(app, command=select_input_file, text="Browse...")

Text(app, text="Output file name:")

output_file = TextBox(app, width=50)

PushButton(app, command=select_output_file, text="Browse...")

def analyze_protein():

    input_path = input_file.value

    output_path = output_file.value

    if not input_path or not output_path:

        info("Error", "Please select input and output files")

        return

    if not os.path.isfile(input_path):

        info("Error", f"Input file '{input_path}' does not exist")

        return

    with open(input_path, "r") as f:

        protein_sequence = f.read().strip()

    aa_count = {}

    for aa in amino_acids:

        aa_count[aa] = protein_sequence.count(aa)

    total_aa = sum(aa_count.values())

    with open(output_path, "w") as f:

        f.write("# Protein Composition\n\n")

        f.write("Amino Acid | Count | Percentage\n")

        f.write("--- | --- | ---\n")

        for aa, count in aa_count.items():

            percentage = (count / total_aa) * 100

            f.write(f"{amino_acids[aa]} | {count} | {percentage:.2f}%\n")

    info("Success", f"Output written to '{output_path}'")

PushButton(app, command=analyze_protein, text="Analyze Protein")

app.display()

'''

V1:

This code uses the tkinter library to create file dialogs for selecting the 

input and output files, and the guizero library to create a simple GUI with 

text boxes and buttons. The analyze_protein function reads the protein 

sequence from the input file selected by the user, analyzes its amino acid 

composition using the same code as before, and saves the result in the 

output file selected by the user.

'''

'''

V2: 

This code adds a check for the existence of the input file, and displays an 

error message if it doesn't exist. It also displays a success message with 

the output file name when the analysis is completed and the output file is 

written.

'''

'''

V3:

This version does not recognize the ".txt" or ".pep" files and they remain 

gray. I am not sure if this is due to this code or the Macintosh.

It's possible that the issue is related to the file types not being 

recognized by the file dialog box. You can try adding the file types 

explicitly to the filetypes argument of the askopenfilename() and 

asksaveasfilename() functions like this:

from tkinter import filedialog

input_file = filedialog.askopenfilename(initialdir="/", title="Select file", filetypes=(("text files", "*.txt"), ("pep files", "*.pep"), ("all files", "*.*")))

output_file = filedialog.asksaveasfilename(initialdir="/", title="Save file", filetypes=(("text files", "*.txt"), ("all files", "*.*")))

'''

import os

import tkinter as tk

from tkinter import filedialog

from guizero import App, Text, TextBox, PushButton, info

amino_acids = {'A': 'Alanine', 'C': 'Cysteine', 'D': 'Aspartic Acid', 'E': 

'Glutamic Acid',

               'F': 'Phenylalanine', 'G': 'Glycine', 'H': 'Histidine', 'I': 

'Isoleucine',

               'K': 'Lysine', 'L': 'Leucine', 'M': 'Methionine', 'N': 

'Asparagine',

               'P': 'Proline', 'Q': 'Glutamine', 'R': 'Arginine', 'S': 

'Serine',

               'T': 'Threonine', 'V': 'Valine', 'W': 'Tryptophan', 'Y': 

'Tyrosine'}

def select_input_file():

    root = tk.Tk()

    root.withdraw()

    file_path = filedialog.askopenfilename(filetypes=[("Text files", 

"*.txt;*.pep")])

    input_file.value = file_path

def select_output_file():

    root = tk.Tk()

    root.withdraw()

    file_path = filedialog.asksaveasfilename(defaultextension=".md")

    output_file.value = file_path

app = App(title="Protein Analysis")

Text(app, text="Select input file:")

# input_file = TextBox(app, width=50)

input_file = filedialog.askopenfilename(initialdir="/", title="Select file", filetypes=(("text files", "*.txt"), ("pep files", "*.pep"), ("all files", "*.*")))

PushButton(app, command=select_input_file, text="Browse...")

Text(app, text="Output file name:")

# output_file = TextBox(app, width=50)

output_file = filedialog.asksaveasfilename(initialdir="/", title="Save file", filetypes=(("text files", "*.txt"), ("all files", "*.*")))

PushButton(app, command=select_output_file, text="Browse...")

def analyze_protein():

    input_path = input_file.value

    output_path = output_file.value

    if not input_path or not output_path:

        info("Error", "Please select input and output files")

        return

    if not os.path.isfile(input_path):

        info("Error", f"Input file '{input_path}' does not exist")

        return

    with open(input_path, "r") as f:

        protein_sequence = f.read().strip()

    aa_count = {}

    for aa in amino_acids:

        aa_count[aa] = protein_sequence.count(aa)

    total_aa = sum(aa_count.values())

    with open(output_path, "w") as f:

        f.write("# Protein Composition\n\n")

        f.write("Amino Acid | Count | Percentage\n")

        f.write("--- | --- | ---\n")

        for aa, count in aa_count.items():

            percentage = (count / total_aa) * 100

            f.write(f"{amino_acids[aa]} | {count} | {percentage:.2f}%\n")

    info("Success", f"Output written to '{output_path}'")

PushButton(app, command=analyze_protein, text="Analyze Protein")

app.display()

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