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
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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

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";
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see the perdoc on system in perlfunc for more details

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.

#!/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
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Try your script this way of checking the exit status of your python script.

---

All is well

Also make sure you close your files in sub1.

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?