Question

Given these inputs:

my $init_seq = 'AAAAAAAAAA' #length 10 bp  my $sub_rate = 0.003; my $nof_tags = 1000; my @dna = qw( A C G T ); 

I want to generate:

1. One thousand length-10 tags

2. Substitution rate for each position in a tag is 0.003

Yielding output like:

AAAAAAAAAA AATAACAAAA ..... AAGGAAAAGA # 1000th tags 

Is there a compact way to do it in Perl?

I am stuck with the logic of this script as core:

#!/usr/bin/perl  my $init_seq = 'AAAAAAAAAA' #length 10 bp  my $sub_rate = 0.003; my $nof_tags = 1000; my @dna = qw( A C G T );      $i = 0;     while ($i < length($init_seq)) {         $roll = int(rand 4) + 1;       # $roll is now an integer between 1 and 4          if ($roll == 1) {$base = A;}         elsif ($roll == 2) {$base = T;}         elsif ($roll == 3) {$base = C;}         elsif ($roll == 4) {$base = G;};          print $base;     }     continue {         $i++;     } 

Answer 1

As a small optimisation, replace:

    $roll = int(rand 4) + 1;       # $roll is now an integer between 1 and 4      if ($roll == 1) {$base = A;}     elsif ($roll == 2) {$base = T;}     elsif ($roll == 3) {$base = C;}     elsif ($roll == 4) {$base = G;}; 

with

    $base = $dna[int(rand 4)];