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

In reply to Re^3: system() issue by Anonymous Monk
in thread system() issue by Anonymous Monk

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