Splitting string (regex) while keeping the separator?

Cantello has asked for the wisdom of the Perl Monks concerning the following question:

Hey all, I am trying to split a string into different parts, based on content (a protein sequence digested by enzymes cutting at different amino acids). I have tried:

my $a = "AAAAXRXAAAAAXKXAAAAAXRPXAAA"  # sample sequence
@digested0 = split(/[KR](?!P)/, $orf); # cut at every K or R, except i
+f followed by a P
print join("\n",@digested0);
[download]

The output is:

AAAAX
XAAAAAX
XAAAAAXRPXAAA
[download]

It's basically correct but it should be

AAAAXR
XAAAAAXK
XAAAAAXRPXAAA
[download]

i.e. keeping the separator "K" or "R". How could I achieve this? There probably is a regexp for that as well, I'm just too blind to find it... Thanks! :-)

Comment on Splitting string (regex) while keeping the separator? Select or Download Code

Replies are listed 'Best First'.
Re: Splitting string (regex) while keeping the separator? by moritz (Cardinal) on May 03, 2010 at 14:08 UTC
If you want to have the delimiter as a separate list item, then use capturing parenthesis around it. If you want to have it attached to the previous item, you need to make it a zero-width look-behind: `split(/(?<=[KR])(?!P)/, $a);` [download] Also you have a few errors in your script that prevent the snippet you posted from producing the output you show. (Mis-named variables, missing semicolon). Perl 6 - links to (nearly) everything that is Perl 6.	[reply] [d/l]
Re: Splitting string (regex) while keeping the separator? by AnomalousMonk (Archbishop) on May 03, 2010 at 16:04 UTC
Note that split passes through the original string if the split pattern never matches. This condition should probably be checked if not wanted. `>perl -wMstrict -le "my $orf = 'AAAAXXAAAAAXXAAAAAXPXAAA'; my @digested0 = split /(?<=[KR](?!P))/, $orf; print for @digested0; " AAAAXXAAAAAXXAAAAAXPXAAA` [download] Here's an `m//` solution without this drawback: `>perl -wMstrict -le "my $a = 'AAAAXRXAAAAAXKXAAAAAXRPXAAA'; my $cut = qr{ [KR] (?!P) }xms; my $digest = qr{ .? $cut \| (?<= $cut) . \z }xms; my @digested = $a =~ m{ $digest }xmsg; print qq{'$_'} for @digested; $a = 'AAAXXXPPPAAAXXXAAAPPPAAA'; @digested = $a =~ m{ $digest }xmsg; print '@digested empty' unless @digested; " 'AAAAXR' 'XAAAAAXK' 'XAAAAAXRPXAAA' @digested empty` [download]	[reply] [d/l] [select]
Re: Splitting string (regex) while keeping the separator? by Anonymous Monk on May 03, 2010 at 14:50 UTC
`$ perl -le' my $orf = "AAAAXRXAAAAAXKXAAAAAXRPXAAA"; my @digested0 = split /(?<=[KR](?!P))/, $orf; print for @digested0; ' AAAAXR XAAAAAXK XAAAAAXRPXAAA` [download]	[reply] [d/l]
Re: Splitting string (regex) while keeping the separator? by Sinistral (Monsignor) on May 03, 2010 at 20:17 UTC
If you haven't already heard of the Bioperl site you should head on over there and see about already optimized and tested solutions for the type of task you are trying to accomplish. In particular (I am not a bio-person), you should look on Bioperl scripts page.	[reply]
Re^2: Splitting string (regex) while keeping the separator? by Cantello (Novice) on May 04, 2010 at 05:45 UTC
Thanks guys, that was really awesome help (even though I made some mistakes asking; sorry for that)! I will work through the examples you've given and also head over to the bioperl site. Thanks again... :-)	[reply]
Re: Splitting string (regex) while keeping the separator? by Anonymous Monk on May 03, 2010 at 14:09 UTC
Read perlintro and use capturing parentheses.	[reply]