Re^3: system() issue

Sorry, you will have to forgive me, I'm biologist with only a little computer knowledge. Here's a bit of code:

#!/usr/bin/perl -w
[download]

use strict;
&sub1; #generates a text file (rep_set.txt)
system('python //macqiime/QIIME/bin/assign_taxonomy.py -i rep_set.txt 
+-o .'); #generates second txt file
&sub2; #reads the second text file
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So, all three work on their own, but when I try to run them together, sub2 gives me a blank output even though the first two parts generate the appropriate files. I'm hoping that I am simply using system() wrong... The subroutines simply open a txt file, capture some data from it, and print it out in a different format. I can provide them if need be, but since they work fine individually, I've left them out for simplicity

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Re^4: system() issue by wazat (Monk) on Dec 13, 2013 at 06:02 UTC
See the response from vinoth.ree. system() has a return value. A return value of 0 is good. Other return values indicate various types of problems. One thing you can do is print the value returned by system. `my $rc = system( 'python //macqiime/QIIME/bin/assign_taxonomy.py -i re +p_set.txt -o .'); print "system returned $rc, \$? is $?\n";` [download] see the perdoc on system in perlfunc for more details	[reply] [d/l]
Re^4: system() issue by Anonymous Monk on Dec 13, 2013 at 05:49 UTC
We still don't have enough information. There's no obvious problem. Like vinoth.ree says, try checking for errors. I like to use this pattern with `system`: `system(...) == 0 or die;` Maybe `sub2` is failing to open its input file. Always error-check opens as well. `open FOO, 'foo.txt' or die;` In a finished script, it's nice to have some kind of error message on the `die` `open FOO, '<', $filename or die "Can't open $filename: $!;` ... but get that `or die` on there, it can save you a lot of head-scratching.	[reply] [d/l] [select]
Re^4: system() issue by vinoth.ree (Monsignor) on Dec 13, 2013 at 08:08 UTC
`#!/usr/bin/perl -w [download] use strict; &sub1; #generates a text file (rep_set.txt) system('python //macqiime/QIIME/bin/assign_taxonomy.py -i rep_set.txt +-o .'); #generates second txt file if ( $? == -1 ) { print "command failed: $!\n"; } else { printf "command exited with value %d", $? >> 8; } &sub2; #reads the second text file` [download] Try your script this way of checking the exit status of your python script. *All is well*	[reply] [d/l]
Re^4: system() issue by Anonymous Monk on Dec 13, 2013 at 06:28 UTC
Also make sure you `close` your files in `sub1`.	[reply]
Re^4: system() issue by Anonymous Monk on Dec 13, 2013 at 06:01 UTC
This is kind of dumb, but... you're running this on a network drive? What happens if you put a `sleep(10)` after the `system`?	[reply]