I need to generate statistics from a very large text file (1GB+) and need to process the file line by line. I originally had something like this: 
open(FILE, "<$ARGV[0]") || die "$!";
count_bases(20);
count_bases(30);
...
sub count_bases {
seek FILE, 0, SEEK_SET; #reset file pointer
my $min_quality = shift;

foreach $line (<FILE>) #main loop
{ 
  my @tmp_ar = split("\t", $line);
  ... 
  #make comparisons and put #s in hash 
}

[download]

but this ended up being too slow. I run this on a remote server (which I do not have admin) and it always gets killed after locking up the server for a couple of minutes. I looked over a similar script (that I did not write) and noticed that they used while(<>) to read things in. This script was not killed by the server when processing the same large file. So I make the following changes

count_bases(20, $ARGV[1]);
count_bases(30, $ARGV[1]);
...
sub count_bases {
my $min_quality = shift;

while(<>)
{ 
  my @tmp_ar = split();
  ... 
  #make comparisons and put #s in hash 
}

[download]

This however does not work for the 2nd count_bases call, it just freezes after the 1st. I am guessing that the while(<>) takes from @ARGV and not the values that I pass into the function so after it uses the 1st time it never starts the end.

my questions: why is the implicit open so much faster? is there a way to get implicit open to work twice? is there a way to make the 1st way fast without implicit open?

thanks

In reply to Efficiently processing a file by Anonymous Monk

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