Hey,

So, I'm basically trying to write a script that cuts a DNA sequence at specific points. I'm able to find the correct sequence within the string, but I can't for the life of me figure out how to split the string at the right site. Here's my code so far: 

use strict;

use Getopt::Std;  #Invokes Get options package
our ($opt_c,$opt_e);
getopts('ce:');


my @seq = <>;
chomp(@seq);
my $seq = join("", @seq);


our %re = (
      'BamHI'  => 'GGATCC 1', # G | GATCC
      'EcoRI'  => 'GAATTC 1', # G | AATTC
      'EcoRII' => 'CCWGG 0',  #   | CCWGG
);

my @enz = split(/\b(\s+)\b/,$re{$opt_e});
my $enzseq = $enz[0];
my $cut = $enz[2];
print "The restriction site is: $enzseq\n\n";

while($seq =~ /($enzseq)/ig) {
    my $site = pos($seq),"\n";
    print "$site\n";
}

[download]
Right now, it prints the locations of where to split the sequence, but I'm not exactly sure how to split the string at these specific location into fragments. For instance, if the string is 6000 characters, and the search string is found at 500, 1000, 2000, 4000, 5000, I want to store/print: (500, 500, 1000, 2000, 1000, 1000).

Any help would be greatly appreciated, Thanks.

~~~~~~~~~~

the current code prints: 

The input sequence length is 48502

The restriction site is: GAATTC

21231
26109
31752
39173
44977

[download]

So, basically, I want to cut at each of those sites, so the fragments should have a length of 21231, (26109-21231), etc, where you subtract each shorter one from the longer one, where the last one is (48502-44977)

In reply to splitting a string by rkenshin09

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