"""
CSCI146 Test Project 1

Name: <Your name>
Section: <Your Section>
"""

# TODO: Implement your functions here

def read_fasta(filename):
    """
    Read a single DNA sequence from a FASTA-formatted file
    
    For example, to read the sequence from a file named "X73525.fasta.txt"
    >>> sequence = read_fasta("X73525.fasta.txt")
    
    Args:
        filename: Filename as a string
        
    Returns: Upper case DNA sequence as a string
    """
    with open(filename, "r") as file:
        # Read (and ignore) header line
        header = file.readline()
        # Read sequence lines
        sequence = ""
        for line in file:
            sequence += line.strip()
        return sequence.upper()


def filter_orfs(orfs, min_length):
    """
    Filter ORFs to have a minimum length
    
    Args:
        orfs: List of candidate ORF sequences
        min_length: Minimum length for an ORF
    
    Returns:
        A new list containing only ORF strings longer than min_length bases
    """
    filtered_orfs = []
    for orf in orfs:
        if len(orf) > min_length:
            filtered_orfs.append(orf)
    return filtered_orfs


def write_fasta(filename, orfs):
    """
    Write list of ORFs to a FASTA formatted text file.
    
    For example, to save a list of orfs assigned to the variable my_orfs to a
    file named "genes.txt"
    >>> write_fasta("genes.txt", my_orfs)
    
    Args:
        filename: Filename as a string. Note that any existing file with this name
            will be overwritten.
        orfs: List of ORF sequences to write to the file
    """
    with open(filename, "w") as file:
        for i in range(len(orfs)):
            # A FASTA entry is a header line that begins with a '>', and then the sequence on the next line(s)
            print(">seq" + str(i), file=file)
            print(orfs[i], file=file)

           
if __name__ == "__main__":
    # If you want perform the steps for creating genes.txt as part of your
    # program, implement that code here. It will run every time you click the
    # green arrow, but will be ignored by Gradescope.
    pass