How to redirect 'print' output to a file u

Question

I want to redirect the print to a .txt file using python. I have a 'for' loop, which will 'print' the output for each of my .bam file while I want to redirect ALL these output to one file. So I tried to put

 f = open('output.txt','w'); sys.stdout = f

at the beginning of my script. However I get nothing in the .txt file. My script is:

#!/usr/bin/python

import os,sys
import subprocess
import glob
from os import path

f = open('output.txt','w')
sys.stdout = f

path= '/home/xug/nearline/bamfiles'
bamfiles = glob.glob(path + '/*.bam')

for bamfile in bamfiles:
    filename = bamfile.split('/')[-1]
    print 'Filename:', filename
    samtoolsin = subprocess.Popen(["/share/bin/samtools/samtools","view",bamfile],
                                  stdout=subprocess.PIPE,bufsize=1)
    linelist= samtoolsin.stdout.readlines()
    print 'Readlines finished!'
    ........print....
    ........print....

So what's the problem? Any other way besides this sys.stdout?

I need my result look like:

Filename: ERR001268.bam
Readlines finished!
Mean: 233
SD: 10
Interval is: (213, 252)

Answer 1

The easiest solution isn't through python; its through the shell. From the first line of your file (#!/usr/bin/python) I'm guessing you're on a UNIX system. Just use print statements like you normally would, and don't open the file at all in your script. When you go to run the file, instead of

./script.py

to run the file, use

./script.py > <filename>

where you replace <filename> with the name of the file you want the output to go in to. The > token tells (most) shells to set stdout to the file described by the following token.

One important thing that needs to be mentioned here is that "script.py" needs to be made executable for ./script.py to run.

So before running ./script.py,execute this command

chmod a+x script.py (make the script executable for all users)

Answer 2

You can redirect print with the >> operator.

f = open(filename,'w')
print >>f, 'whatever'     # Python 2.x
print('whatever', file=f) # Python 3.x

In most cases, you're better off just writing to the file normally.

f.write('whatever')

or, if you have several items you want to write with spaces between, like print:

f.write(' '.join(('whatever', str(var2), 'etc')))

Answer 3

if ur using linux i suggest u to use tee command the implementation goes like this python python_file.py |tee any_file_name.txt if u dont want to change anything in the code ,i think this might be the best possible solution ,u can also implement logger but u need do some changes in the code.

Answer 4

Changing the value of sys.stdout does change the destination of all calls to print. If you use an alternative way to change the destination of print, you will get the same result.

Your bug is somewhere else:

• it could be in the code you removed for your question (where does filename come from for the call to open?)
• it could also be that you are not waiting for data to be flushed: if you print on a terminal, data is flushed after every new line, but if you print to a file, it's only flushed when the stdout buffer is full (4096 bytes on most systems).