git-version-ctrl.txt

# 3
gene_list = ["AT1G0010", "AT1G0020", "AT1G0030", "AT1G0040", "AT1G0050", 
"AT1G0060", "AT1G0070", "AT1G0080"]
for genes in gene_list:
    print(genes)
	

#5 
# Create reverse DNA sequence
def reverse(s):
    """
    Function to create a DNA reverse sequence, starting from the end.

    Parameters:
    s (str): A string is taken as the input

    Returns:
    s (str): A reverse version of the input string is returned
    """
    return (s[::-1])
# Complement function
def complement(s):
    """
    The function creates a complementary DNA sequence

    Parameters:
    s(str): A string of DNA sequences is taken as the input

    Returns:
    Letters (str): A list consisting of the complementary DNA sequence
    """
    # A dictionary that associates each string character (nucleotide) to its complementary character: A to T, C to G
    basecomplement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'a': 't', 'c': 'g', 
'g': 'c', 't': 'a', 'M': 'K', 'K': 'M', 'R': 'Y', 'Y': 'R', 'W': 'W', 'S': 'S', 
'V': 'B', 'B': 'V', 'H': 'D', 'D': 'H', 'N': 'N', '-': '-' }
    # Create a list using the input string
    letters = list(s)
    # For loop to iterate through each base/letter in the list
    letters = [basecomplement[base] for base in letters]
    # Return statement to join each character in the list
    return ''.join(letters)
# Reverse and Complementary function
def revcom(s):
    """
    The function is a combination of the reverse and complement functions. 
    The input string is first reversed from the end, then the complementary string of the reversed string is produced

    Parameters:
    s(str): input

    Return:
    s (str): reversed and complementary string
    """
    return complement(s[::-1])

#6
# Write a function that will parse a fasta file and produce a reverse complement.
def fasta_reverse_complement(fasta_file: str) -> dict[str, str]:
    """
    Parses a FASTA file and produces the reverse complement of each DNA sequence.

    Parameters:
    fasta_file (str): The path to the FASTA file.

    Returns:
    dict[str, str]: A dictionary where keys are sequence identifiers (keys) and values are their reverse complements.
    """
    # Create an empty dictionary to query
    reverse_complements = {}

    # Open the file
    with open(fasta_file, 'r') as file:
        sequence_id = None
        # Create an empty list
        sequence = []

        # For Loop to iterate through the lines
        for line in file:
            # Strip whitespaces
            line = line.strip()
            # IF statement to specify a header
            if line.startswith('>'):
                # If we have a previous sequence, process it
                if sequence_id is not None:  
                    # join the sequences
                    full_sequence = ''.join(sequence)
                    # Use revcom function
                    reverse_complements[sequence_id] = revcom(full_sequence)
                
                # Get the sequence identifier
                sequence_id = line[1:]  
                # Reset the sequence list for the new sequence
                sequence = []  
            else:
                # append the sequences
                sequence.append(line) 

        # Process the last sequence in the file
        if sequence_id is not None:
            full_sequence = ''.join(sequence)
            reverse_complements[sequence_id] = revcom(full_sequence)

    return reverse_complements

# Example usage:
fasta_file_path = 'Downloads/AB_test_dta.fasta'
reverse_complement_dict = fasta_and_reverse_complement(fasta_file_path)
for seq_id, rev_comp in reverse_complement_dict.items():
    print(f"{seq_id}: {rev_comp}")


#7

def sort_numerical_list(numbers_list):
    """
    This function takes a list of numerical strings and returns a list of sorted integers.

    Parameters:
    numbers_list (list): A list of strings representing numbers.

    Returns:
    list: A sorted list of integers in numerical order.
    """
    # Convert strings to integers
    numbers_as_integers = [int(num) for num in numbers_list]
    
    # Sort the list
    sorted_numbers = sorted(numbers_as_integers)
    
    return sorted_numbers

# Corrected input list
numbers_list = ['98', '67', '112', '4', '45', '78', '99', '100', '-1', '7', '0']

# Call the function and print the result
sorted_numbers = sort_numerical_list(numbers_list)
print(sorted_numbers)

# 8
# Write a function that draws a number at random from the list given in Question 7
# Import random module
import random
# Create a function to draw numbers randomly from a list
def draw_random_number(numbers_list):
    """
    This function draws a random number from the given list of numerical strings.

    Parameters:
    numbers_list (list): A list of strings representing numbers.

    Returns:
    int: A randomly selected number from the list.
    """
    # Convert strings to integers because the list here has numerical strings
    numbers_as_ints = [int(num) for num in numbers_list]
    
    # Draw a random number
    random_number = random.choice(numbers_as_ints)
    
    return random_number

# Corrected input list
numbers_list = ['98', '67', '112', '4', '45', '78', '99', '100', '-1', '7', '0']

random_number = draw_random_number(numbers_list)
print("Randomly Selected Number:", random_number)