How to redirect print output to a file using python

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 xxx nearline bamfiles  bamfiles   glob glob path       bam    for bamfile in bamfiles      filename   bamfile split      -1      print  Filename    filename     samtoolsin   subprocess Popen   quot  share bin samtools samtools quot   quot view quot  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                     How time flies  Almost 10 years ago I started to work on bioinformatics without any coding skills  Then I gave up my PhD and previous career and becomes a pure software engineer

User · Answer

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  gt   lt filename gt    where you replace  lt filename gt  with the name of the file you want the output to go in to   The  gt  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

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The most obvious way to do this would be to print to a file object  with open  out txt    w   as f      print  gt  gt  f   Filename    filename       Python 2 x     print  Filename    filename  file f      Python 3 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  gt  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

User · Answer

If redirecting stdout works for your problem  Gringo Suave s answer is a good demonstration for how to do it   To make it even easier  I made a version utilizing contextmanagers for a succinct generalized calling syntax using the with statement   from contextlib import contextmanager import sys   contextmanager def redirected stdout outstream       orig stdout   sys stdout     try          sys stdout   outstream         yield     finally          sys stdout   orig stdout   To use it  you just do the following  derived from Suave s example    with open  out txt    w   as outfile      with redirected stdout outfile           for i in range 2               print  i     i    It s useful for selectively redirecting print when a module uses it in a way you don t like  The only disadvantage  and this is the dealbreaker for many situations  is that it doesn t work if one wants multiple threads with different values of stdout  but that requires a better  more generalized method  indirect module access  You can see implementations of that in other answers to this question

User · Answer

Something to extend print function for loops  x   0 while x  lt  5      x   x   1     with open  outputEis txt    a   as f          print x  file f      f close

User · Answer

Don t use print  use logging  You can change sys stdout to point to a file  but this is a pretty clunky and inflexible way to handle this problem   Instead of using print  use the logging module   With logging  you can print just like you would to stdout  or you can also write the output to a file   You can even use the different message levels  critical  error  warning  info  debug  to  for example  only print major issues to the console  but still log minor code actions to a file   A simple example  Import logging  get the logger  and set the processing level   import logging logger   logging getLogger   logger setLevel logging DEBUG    process everything  even if everything isn t printed   If you want to print to stdout   ch   logging StreamHandler   ch setLevel logging INFO    or any other level logger addHandler ch    If you want to also write to a file  if you only want to write to a file skip the last section    fh   logging FileHandler  myLog log   fh setLevel logging DEBUG    or any level you want logger addHandler fh    Then  wherever you would use print use one of the logger methods     print foo  logger debug foo     print  finishing processing   logger info  finishing processing      print  Something may be wrong   logger warning  Something may be wrong      print  Something is going really bad   logger error  Something is going really bad     To learn more about using more advanced logging features  read the excellent logging tutorial in the Python docs

User · Answer

If you are using Linux I suggest you to use the tee command  The implementation goes like this  python python file py   tee any file name txt  If you don t want to change anything in the code  I think this might be the best possible solution  You can also implement logger but you need do some changes in the code

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Python 2 or Python 3 API reference  print  objects  sep      end   n   file sys stdout  flush False   The file argument must be an object with a write string  method  if it is not present or None  sys stdout will be used  Since printed arguments are converted to text strings  print   cannot be used with binary mode file objects  For these  use file write      instead    Since file object normally contains write   method  all you need to do is to pass a file object into its argument  Write Overwrite to File with open  file txt    w   as f      print  hello world   file f   Write Append to File with open  file txt    a   as f      print  hello world   file f

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You can redirect print with the  gt  gt  operator   f   open filename  w   print  gt  gt 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

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This works perfectly   import sys sys stdout open  test txt   w   print   hello   sys stdout close     Now the hello will be written to the test txt file  Make sure to close the stdout with a close  without it the content will not be save in the file

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In python 3  you can reassign print     usr bin python3  def other fn         This will use the print function that s active when the function is called     print  quot Printing from function quot    file name    quot test txt quot  with open file name   quot w  quot   as f out      py print   print  Need to use this to restore builtin print later  and to not induce recursion         print   lambda out str   py print out str  file f out            If you d like  for completeness  you can include args kwargs     print   lambda  args    kwargs   py print  args  file f out    kwargs           print  quot Writing to  s quot    file name        other fn     Writes to file       Must restore builtin print  or you ll get  I O operation on closed file       If you attempt to print after this block     print   py print  print  quot Printing to stdout quot   other fn    Writes to console stdout  Note that the print from other fn only switches outputs because print is being reassigned in the global scope   If we assign print within a function  the print in other fn is normally not affected   We can use the global keyword if we want to affect all print calls  import builtins  def other fn         This will use the print function that s active when the function is called     print  quot Printing from function quot    def main        global print  Without this  other fn will use builtins print     file name    quot test txt quot      with open file name   quot w  quot   as f out           print   lambda  args    kwargs   builtins print  args  file f out    kwargs           print  quot Writing to  s quot    file name            other fn     Writes to file           Must restore builtin print  or you ll get  I O operation on closed file           If you attempt to print after this block         print   builtins print      print  quot Printing to stdout quot       other fn    Writes to console stdout  Personally  I d prefer sidestepping the requirement to use the print function by baking the output file descriptor into a new function  file name    quot myoutput txt quot  with open file name   quot w  quot   as outfile      fprint   lambda pstring   print pstring  file outfile      print  quot Writing to stdout quot       fprint  quot Writing to  s quot     file name

User · Answer

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

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You may not like this answer  but I think it s the RIGHT one  Don t change your stdout destination unless it s absolutely necessary  maybe you re using a library that only outputs to stdout    clearly not the case here    I think as a good habit you should prepare your data ahead of time as a string  then open your file and write the whole thing at once  This is because input output operations are the longer you have a file handle open  the more likely an error is to occur with this file  file lock error  i o error  etc   Just doing it all in one operation leaves no question for when it might have gone wrong   Here s an example   out lines      for bamfile in bamfiles      filename   bamfile split      -1      out lines append  Filename   s    filename      samtoolsin   subprocess Popen    share bin samtools samtools   view  bamfile                                     stdout subprocess PIPE bufsize 1      linelist  samtoolsin stdout readlines       print  Readlines finished       out lines extend linelist      out lines append   n     And then when you re all done collecting your  data lines  one line per list item  you can join them with some   n  characters to make the whole thing outputtable  maybe even wrap your output statement in a with block  for additional safety  will automatically close your output handle even if something goes wrong    out string     n  join out lines  out filename    myfile txt  with open out filename   w   as outf      outf write out string  print  YAY MY STDOUT IS UNTAINTED       However if you have lots of data to write  you could write it one piece at a time  I don t think it s relevant to your application but here s the alternative   out filename    myfile txt  outf   open out filename   w   for bamfile in bamfiles      filename   bamfile split      -1      outf write  Filename   s    filename      samtoolsin   subprocess Popen    share bin samtools samtools   view  bamfile                                     stdout subprocess PIPE bufsize 1      mydata   samtoolsin stdout read       outf write mydata  outf close

[python-2.x] How to redirect 'print' output to a file using python?

Examples related to python-2.x

Examples related to file-writing