Using a regexp to extract sequence fields

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

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Re: Using a regexp to extract sequence fields by McDarren (Abbot) on Feb 13, 2006 at 10:03 UTC
Whenever you have delimited data, you probably want to consider using split. For example: `my $foo = ">blabla1\|anyting1\|blabla2\|anyting2\|blabla3\| "; my @fields = split /\\|/, $foo;` [download] In this case, you said you wanted the 3rd "field", so you would just access it as `$fields[2]` Hope this helps, Darren :)	[reply] [d/l] [select]
Re^2: Using a regexp to extract sequence fields by tamaguchi (Pilgrim) on Feb 13, 2006 at 10:09 UTC
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 $&.	[reply]
Re: Using a regexp to extract sequence fields by svenXY (Deacon) on Feb 13, 2006 at 09:58 UTC
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";` [download] results in: `splitted: blabla2 regexed: blabla2` [download] Regards, svenXY Update:* added regex solution	[reply] [d/l] [select]
Re: Using a regexp to extract sequence fields by Samy_rio (Vicar) on Feb 13, 2006 at 10:04 UTC
Hi tamaguchi, Try this, `use strict; use warnings; $_='>blabla1\|anyting1\|blabla2\|anyting2\|blabla3\|'; if (m/>[^\\|]+\\|[^\\|]+\\|([^\\|]+)\\|/){ print $1; }` [download] Updated Regards, Velusamy R. eval"print uc\"\\c$_\""for split'','j)@,/6%@0%2,`e@3!-9v2)/@\|6%,53!-9@2~j';	[reply] [d/l] [select]
Re^2: Using a regexp to extract sequence fields by svenXY (Deacon) on Feb 13, 2006 at 10:09 UTC
Hi, why the /si ? It's not necessary at all. Regards, svenXY	[reply]
Re: Using a regexp to extract sequence fields by misterb101 (Sexton) on Feb 13, 2006 at 10:23 UTC
Or of course only with regexp: `my @matches ">blabla1\|anyting1\|blabla2\|anyting2\|blabla3\|" =~ m/[a-zA- +Z0-9]+/xg; print $matches[2];` [download] -- Cheers, Rob	[reply] [d/l]
Re: Using a regexp to extract sequence fields by MCS (Monk) on Feb 13, 2006 at 15:02 UTC
The problem (well not really a problem but given your example, a problem) with Regular Expressions is that they are very specific. In order for us to help you more, we need a little more information Are you just trying to match a specific line of text? (ie 'blabla2') or are you trying to match `blabla[some number]`? If you are looking for an exact string, your best bet is to use split (as per other examples here) and then iterate over the array (say a foreach) and compare each item to your string. Of course you say that 'anything' or 'blabla' are arbitrary sequences, I'm guessing you're not trying to match an exact string but rather a positional thing. In that case, use split and then you will have your data in an array and you can go to any position. `$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.	[reply] [d/l] [select]