Using a regexp to extract sequence fields

[tamaguchi]

I have a sequence that starts with '>' and is delimited by '|' so that the seqence looks..

>blabla1|anyting1|blabla2|anyting2|blabla3|

Now I would need to match for example the subsequence between the second '|' and the third '|' to get 'blabla2' out, unfortunatly my knowledge of regexps has become little rusty could you help me out? I can ofcourse not mach 'anything' or 'blabla' directly since they are arbitrary sequences in reality. Thank you very for any help much.

2006-02-13 Retitled by Arunbear, as per Monastery guidelines
Original title: 'Regexp'

[McDarren]

Whenever you have delimited data, you probably want to consider using split.

For example:

my $foo = ">blabla1|anyting1|blabla2|anyting2|blabla3| ";
my @fields = split /\|/, $foo;

In this case, you said you wanted the 3rd "field", so you would just access it as $fields[2]

Hope this helps,
Darren :)

[tamaguchi]

Yes thank you. I know there are many ways to get for example 'blabla2' out. But the expression should not be used directly for programming. In the context I should use ít it must match the sequence directly so that I get blabla2 out in $&.

[svenXY]

Hi,
I'd do this with split, although regex is possible as well:


#!/usr/bin/perl
use strict;

my $string = '>blabla1|anyting1|blabla2|anyting2|blabla3|';

# with split
my $third = (split(/\|/, $string))[2];

# with regex
my ($third_regexed) = $string =~ /^[^\|]+\|[^\|]+\|([^\|]+)\|.*/;

print "splitted: $third\nregexed: $third_regexed\n";

results in:


splitted: blabla2
regexed: blabla2


Regards,
svenXY

Update: added regex solution

[Samy_rio]

Hi tamaguchi, Try this,

use strict;
use warnings;

$_='>blabla1|anyting1|blabla2|anyting2|blabla3|';

if (m/>[^\|]+\|[^\|]+\|([^\|]+)\|/){
    print $1;    
}

Updated

[svenXY]

Hi,
why the /si ? It's not necessary at all.
Regards,
svenXY

[misterb101]

Or of course only with regexp:



my @matches  ">blabla1|anyting1|blabla2|anyting2|blabla3|" =~ m/[a-zA-
+Z0-9]+/xg;
print $matches[2];

[MCS]

The problem (well not really a problem but given your example, a problem) with Regular Expressions is that they are very specific. In order for us to help you more, we need a little more information

Are you just trying to match a specific line of text? (ie 'blabla2') or are you trying to match blabla[some number]? If you are looking for an exact string, your best bet is to use split (as per other examples here) and then iterate over the array (say a foreach) and compare each item to your string.

Of course you say that 'anything' or 'blabla' are arbitrary sequences, I'm guessing you're not trying to match an exact string but rather a positional thing. In that case, use split and then you will have your data in an array and you can go to any position. $yourarray[2] for 'blabla2' $yourarray[0] for 'blabla1' etc...

If you are looking for 'blabla#' where # is a number you can use the regex: $mystring =~ /blabla\d+/. If you need more information than I've provided, you're going to have to provide more information about your requirements.