How Break The Infinite Loop in Perl Under Redo (generating random number) - algorithm

Question

I intend to generate random number the following step:
Read the data from file (<DATA>)
Generate random numbers as many as the input data lines
The random number should not be generated twice,
e.g. if the rand number generated in loop no x, has been created
before then, recreate the random number.
Here is the code I have which leads to infinite loop.
What's wrong with my logic, and how can I fix it?
#!/usr/bin/perl -w
use strict;
my %chrsize = ('chr1' =>249250621);
# For example case I have created the
# repository where a value has been inserted.
my %done =("chr1 182881372" => 1);
while ( <DATA> ) {
chomp;
next if (/^\#/);
my ($chr,$pos) = split(/\s+/,$_);
# this number has been generated before
# with this: int(rand($chrsize{$chr}));
# hence have to create other than this one
my $newst =182881372;
my $newpos = $chr ."\t".$newst;
# recreate random number
for (0...10){
if ( $done{$newpos} ) {
# INFINITE LOOP
$newst = int(rand($chrsize{$chr}));
redo;
}
}
$done{$newpos}=1;
print "$newpos\n";
}
__DATA__
# In reality there are 20M of such lines
# name positions
chr1 157705682
chr1 19492676
chr1 169660680
chr1 226586538
chr1 182881372
chr1 11246753
chr1 69961084
chr1 180227256
chr1 141449512

Answer 1

You had a couple of errors:
You were setting $newst within your loop every time, so $newpos never took on a new value.
Your inner for loop didn't make sense, because you never actually changed $newpos before checking the condition again.
redo; was working on the inner loop.
Here is a corrected version that avoids redo altogether.
Update: I edited the algorithm a bit to make it simpler.
#!/usr/bin/perl -w
use strict;
my $chr1size = 249250621;
my %done;
my $newst;
while ( <DATA> ) {
chomp;
next if (/^\#/);
my ($chr,$pos) = split(/\s+/,$_);
my $newpos;
#This will always run at least once
do {
$newst = int(rand($chr1size));
$newpos = $chr ."\t".$newst;
} while ( $done{$newpos} );
$done{$newpos}=1;
print "$newpos\n";
}
Update 2: while the above algorithm will work, it will get really slow on 20,000,000 lines. Here is an alternative approach that should be faster (There is sort of a pattern to the random numbers it generates, but it would probably ok for most situations).
#!/usr/bin/perl -w
use strict;
my $newst;
#make sure you have enough. This is good if you have < 100,000,000 lines.
use List::Util qw/shuffle/;
my #rand_pieces = shuffle (0..10000);
my $pos1 = 0;
my $offset = 1;
while ( <DATA> ) {
chomp;
next if (/^\#/);
my ($chr,$pos) = split(/\s+/,$_);
$newst = $rand_pieces[$pos1] * 10000 + $rand_pieces[($pos1+$offset)%10000];
my $newpos = $chr ."\t".$newst;
$pos1++;
if ($pos1 > $#rand_pieces)
{
$pos1 = 0;
$offset = ++$offset % 10000;
if ($offset == 1) { die "Out of random numbers!"; }
}
print "$newpos\n";
}

Answer 2

Add a counter to your loop like this:
my $counter = 0;
# recrate
for (0...10){
if ( $done{$newpos} ) {
# INFINITE LOOP
$newst = int(rand($chr1size));
redo if ++$counter < 100; # Safety counter
# It will continue here if the above doesn't match and run out
# eventually
}
}

Answer 3

To get rid of the infinite loop, replace redo with next.
http://www.tizag.com/perlT/perlwhile.php :
"Redo will execute the same iteration over again."
Then you may need to fix the rest of the logic ;).