Re: Shuffling codons

[hippo]

It's an FAQ!

I am uncapable of installing the list utils

List::Util is in core and has been since 5.7.3 so you probably don't even need to install it. Either way, I'd tackle this problem (module installation) if I were in your shoes as fixing it will solve many more problems that just the one in your post.

In what way are you incapable of installing it?

[WouterVG]

Thanks for your reply. I know it is an FAQ, That's where I got the Fisher Yates option from, But unable to correctly implement it in my code..

If I try the list util it doesnt work... My code looks like this

print "enter sequence and signal end with enter followed by ctrl d\n";
$sequence = <STDIN>;
chomp $sequence;
print "sequence inserted : $sequence\n";
@trips = unpack("a3" x (length($sequence)-2), $sequence);
@trips = join(" ", @trips);
 use List::Util 'shuffle';
@shuffled = shuffle(@trips);
print "@shuffled\n";

What is wrong/missing here?

I am incapable of installing the list::utils, I wouldn't know where to unpack them and how to properly install and run them. Do they need to be situated somewhere. I am on perl v5.18.2, so the list utils should already be there you mention?

How would I implement the fisher Yates algorithm correctly?

[pryrt]

perl v5.18.2 came after perl v5.7.3, so yes, it should be installed for you. However, the name is List::Util, not list::utils. The following shows that list::utils doesn't exist, but that List::Util exists and has been in core since v5.7.3:

pryrt@debianvm:~$ perl -Mlist::utils -le 'print "OK"'
Can't locate list/utils.pm in @INC (you may need to install the list::
+utils module) (@INC contains: ./blib/lib /home/pryrt/perl5/perlbrew/p
+erls/perl-5.20.3/lib/site_perl/5.20.3/i686-linux /home/pryrt/perl5/pe
+rlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3 /home/pryrt/perl5/perlb
+rew/perls/perl-5.20.3/lib/5.20.3/i686-linux /home/pryrt/perl5/perlbre
+w/perls/perl-5.20.3/lib/5.20.3 .).
BEGIN failed--compilation aborted.
pryrt@debianvm:~$ perl -MList::Util -le 'print "OK"'
OK
pryrt@debianvm:~$ corelist List::Util

Data for 2015-09-12
List::Util was first released with perl v5.7.3

... Besides, if your example code, which included use List::Util 'shuffle'; compiled at all, then you already knew you had it installed properly.

Oh, there, that's what you're doing wrong: @trips = join(" ", @trips);. You just replaced the contents of the @trips array with a single value, which is a string which joins all the old elements of @trips with a space. I think what you want is more akin to:

#!/usr/bin/env perl
use warnings;
use strict;

print "enter sequence and signal end with enter followed by ctrl d\n";
my $sequence = <STDIN>;
chomp $sequence;
print "sequence inserted : $sequence\n";
my @trips = unpack("a3" x (length($sequence)-2), $sequence);
local $" = ", ";
print "unshuffled: (@trips)\n";
use List::Util 'shuffle';
my @shuffled = shuffle(@trips);
print "shuffled: (@shuffled)\n"; 
__END__

__RESULTS__
enter sequence and signal end with enter followed by ctrl d
GATTACCAT
sequence inserted : GATTACCAT
unshuffled: (GAT, TAC, CAT, , , , )
shuffled: (, , GAT, TAC, CAT, , )

[hippo]

If I try the list util it doesnt work

Not enough information there. Error message? Segfault? Compilation error?

What is wrong/missing here?

This line:

@trips = join(" ", @trips);

ruins it. What do you understand this line to be doing? Without it I get at least some shuffling which may or may not be what you want:

#!/usr/bin/env perl 
use strict;
use warnings;
use List::Util 'shuffle';

print "enter sequence and signal end with enter followed by ctrl d\n";
my $sequence = <STDIN>;
chomp $sequence;
print "sequence inserted : $sequence\n";
my @trips = unpack("a3" x (length($sequence)-2), $sequence);
my @shuffled = shuffle(@trips);
print "@shuffled\n";

which gives:

$ perl /tmp/shuf.pl 
enter sequence and signal end with enter followed by ctrl d
aaabbbcccddd
sequence inserted : aaabbbcccddd
ccc aaa    ddd  bbb

I am on perl v5.18.2, so the list utils should already be there you mention?

Yes.