with open("file1.txt") as input_file:
    with open("file2.txt") as output_file:
        for line in input_file:
            if line.startswith(">"):
                name = line.strip()
                # do something interesting with the name
                output_file.write(name+"\n")
            else:
                data = line.strip().split(";")
                # do something interesting with the data
                output_file.write(data+"\n")

with open("file2.txt") as input_file:
    with open("file3.txt") as output_file:
        for line in input_file:
            if line.startswith(">"):
                name = line.strip()
                # do something interesting with the name
                output_file.write(name+"\n")
            else:
                data = line.strip().split(";")
                # do something interesting with the data
                output_file.write(data+"\n")

########################################################

first_data = []
with open("file1.txt") as input_file:
    for line in input_file:
        if line.startswith(">"):
            name = line.strip()
            # do something interesting with the name
        else:
            data = line.strip().split(";")
            # do something interesting with the data
            row = (name, data) # tuple!
            first_data.append(row)

second_data = []
for name, data in first_data:
    new_data = # do something to data to make new_data
    row = (name, new_data)
    second_data.append(row)

with open("file3.txt") as output_file:
    for name, data in second_data:
        # do something interesting with the name and data
        output_file.write(name+"\n")
        output_file.write(data+"\n)