Re: Regular expression problems

if($readingframe2 =~ /MHGR/){
        print "$1\n";
        ($protein)= $readingframe2 =~ /MHGR/;
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$1 contains what you capture with parens: no parens here in regex, so nothing in $1.
What would you like to find in $prottein ?

example:
$ perl -e '$s="pilpoil";if ($s=~/p(.)lp(.)il/) { print "h".$1."h".$2;}
+'
hiho
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Comment on Re: Regular expression problems Select or Download Code

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Re^2: Regular expression problems by rattytatty (Initiate) on Apr 24, 2012 at 08:22 UTC
Thanks for the help. I used this as an example but I will be using it to find an ORF (A Start codon'M', followed by any of the rest of the Amino Acids until a Stop codon'_' I think that will be: `=~/(M)[GAVLIFWPSTCYNQDEKRH]+(_)/` or `=~/(M[GAVLIFWPSTCYNQDEKRH]+_)/` I'm not sure but I will try both. Thanks again.	[reply] [d/l] [select]
Re^3: Regular expression problems by brx (Pilgrim) on Apr 24, 2012 at 14:16 UTC
You can want to add 'M' and '_' in parens to capture in one shot or concatanate 'M'.$1.'_' depending of what you want to do. One way to do it: `#!/usr/bin/perl -w use strict; my $seqnum=1; while (my $seq=<DATA>) { chomp $seq; print "sequence #",$seqnum++,":\n"; while ($seq =~ /M([GAVLIFWPSTCYNQDEKRH]+)_/g) { print "\t",$1,"\n"; # or: print "\t","M${1}_","\n"; } } __DATA__ MHGRRRRRRRRRRRRRRRRRRRRRRRRRRRRRD_MHGRRRRRRRRD_ CMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVTECMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVT AWPPPPPPPPPPPPPPPPPPPPPPPPPPPPP_LNAWPPPPPPPPPPPPPPPPPPPPPPPPPPPPP_L FOOBARMNOTTHISONE_XYZMTHISYES_MTHISNOT_` [download]	[reply] [d/l]