Not looking bad for as far as I can see. If the example file is accurate for the lengths of the input files, then I don't forsee any real problems, though others may of course disagree.
Naming:
cmdline is quite a... short name for a function. I'd think cmd_line for snake_case convention. However, what it does is create what's basically a text file in a bytes buffer by means of running a program. While you could call that a command line execution if you're working from a terminal, I'd name it after the invoked program, or something more generic like get_input_data. Since generic is always survivable at best, I'd pick something like get_needle_results or something like that.
For a module like subprocess which you can guess does creative things dependent on what platform you're on, it's always advisable to grab the docs:
args should be a sequence of program arguments or else a single string. By default, the program to execute is the first item in args if args is a sequence. If args is a string, the interpretation is platform-dependent and described below. See the shell and executable arguments for additional differences from the default behavior. Unless otherwise stated, it is recommended to pass args as a sequence.
And your platform matters - a lot. If you never switch platform or needle implementation, then you can do what you're doing, but if not you're risking a collossal headache with potentially giving it wrong arguments. Therefore, you might want to restructure it to a list of arguments.
And if you don't, use f-strings, the best invention since the list comprehension:
cmd = 'needle -datafile EBLOSUM62 -auto Y' + ' -asequence ' + file1 +' -bsequence ' + file2 + ' -sprotein1 Y -sprotein2 Y ' + ' -auto -stdout'
# Becomes:
cmd = f'needle -datafile EBLOSUM62 -auto Y -asequence {file1} -bsequence {file2} -sprotein1 Y -sprotein2 Y -auto -stdout'
Which is shorter and more readable.
results = cmdline(cmd)
results = results.decode("utf-8")
These can be combined:
results = cmdline(cmd).decode("utf-8")
So can these:
identity = re.search(r"\d{1,3}\.\d*\%", results)
identity = identity.group()
identity = identity.replace('%', '')
# New:
identity = re.search(r"\d{1,3}\.\d*\%", results).group().replace('%', '')
if blast_two_sequences(file1, file2) is not None:
identity, result = blast_two_sequences(file1, file2)
And ouch... you're actually running your entire program twice. If your needle executions are counted, you might have noticed this. You should refactor this to:
output = blast_two_sequences(file1, file2)
if output is not None:
identity, result = output
# Or if you work with Python 3.8+
if output := blast_two_sequences(file1, file2) is not None:
identity, result = output
You should also put a guard around the actual execution, so that a later scripter can import your functions and use them without executing your script on import:
if __name__ == "__main__":
file1 = "/Users/catuf/Desktop/file1.txt"
file2 = "/Users/catuf/Desktop/file2.txt"
if output := blast_two_sequences(file1, file2) is not None:
identity, result = output
Exceptions:
There's a small issue you have - you have a bare except in your code. That means that if weird stuff happens, your program will just ignore it and return none. In your case, I would recommend removing the try: statement completely, and you'll be informed about any problems that arise. If you're watching out for specific Exceptions, narrow your except: to those, and preferably restrict your try/except to directly around the origin lines of these Exceptions.
This will obsolete your None check on the outside. Exceptions showing up on your screen is a good thing - it means you'll be notified when the unexpected happens and you have some unknown error - because now you can go fix it.
