CODEWITHSUNDEEP
regexperlbioinformatics
Alexander Li
Alexander Li

Reputation: 1

How to match the same pattern in a string(one line) and perform the same action again

suppose $dna = "aaaaccccttttaaaaggggaaaacccccaaaaggggaaaacccctttttttt"

I want to cut between each aaaa & cccc in thee string and put on new line. For example, I want to get

aaaa
ccccttttaaaaggggaaaa
cccccaaaaggggaaaa
cccctttttttt

my code:

 if ($DNA =~ /(.*)$match(.*)/) { # $match would be aaaacccc together
               my $fragment1 = $1.$pre-match; # pre-match is aaaa
               my $fragment2 = $post-match.$2; # post-match is cccc
               print"$fragment1\n$fragment2\n";

I want to cut on every match.

Very Important, dna CANNOT be cut if only post-match. There must be a pre-match

Let me know what I am doing wrong. Thank you

Upvotes: 0

Views: 66

Answers (3)

heathobrien
heathobrien

Reputation: 1027

I think the simplist way is to add line breaks with a substitution:

$dna =~ s/aaaacccc/aaaa\ncccc/g;

Upvotes: 0

arco444
arco444

Reputation: 22821

This will do what you want:

$dna = "aaaaccccttttaaaaggggaaaacccccaaaaggggaaaacccctttttttt";
$dna =~ s/(.*?)(cccc.*?)/$1\n$2/g;

print "$dna\n";

The regex will add a newline before every cccc

Outputs:

aaaa
ccccttttaaaaggggaaaa
cccccaaaaggggaaaa
cccctttttttt

Upvotes: 1

Patrick J. S.
Patrick J. S.

Reputation: 2935

One solution is to split the string and join it with "\n":

use warnings;
use strict;
use 5.01;

my $dna = "aaaaccccttttaaaaggggaaaacccccaaaaggggaaaacccctttttttt";
my ($split_left, $split_right) = ('aaaa','cccc');

say join "\n", split /(?<=$split_left)(?=$split_right)/, $dna;

Post match and pre match are predefined terms in perl and mean the whole string before and after the last match (you can access them with the /p flag via ${^PREMATCH} and ${^POSTMATCH}). Also variable names in perl can't contain - since it is an operator, use _ or camelCasing instead.

Upvotes: 0

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