The most obvious way to do this would be to print to a file object:
with open('out.txt', 'w') as f:
print('Filename:', filename, file=f) # Python 3.x
print >> f, 'Filename:', filename # Python 2.x
However, redirecting stdout also works for me. It is probably fine for a one-off script such as this:
import sys
orig_stdout = sys.stdout
f = open('out.txt', 'w')
sys.stdout = f
for i in range(2):
print('i = ', i)
sys.stdout = orig_stdout
f.close()
Since Python 3.4 there’s a simple context manager available to do this in the standard library:
from contextlib import redirect_stdout
with open('out.txt', 'w') as f:
with redirect_stdout(f):
print('data')
Redirecting externally from the shell itself is another option, and often preferable:
./script.py > out.txt
Other questions:
What is the first filename in your script? I don’t see it initialized.
My first guess is that glob doesn’t find any bamfiles, and therefore the for loop doesn’t run. Check that the folder exists, and print out bamfiles in your script.
Also, use os.path.join and os.path.basename to manipulate paths and filenames.