positions of multiple matches

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

Hello dear PerlMonks, I'm trying to match a certain pattern in a DNA sequence and retrieve the position of the match. This wouldn't create a problem, but I don't know how to use the pos() function on an array. I also don't know how to use $- with an unknown amount of matches. This is what I have so far:

@TATA = ($seq =~ m/TATA[A|T][A|T][A|T|G]/i)
 $number_of_TATA = @TATA;
 if ($number_of_TATA > 0){
    print "The positions of the TATA box are:";

  foreach (@TATA){

    $TATA_position=pos($TATA)-7;
    print $TATA_position."\n";
 }
[download]

I'd greatly appreciate the help! thanks a lot!

Comment on positions of multiple matches Download Code

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Re: positions of multiple matches by AnomalousMonk (Archbishop) on Nov 05, 2011 at 15:31 UTC
`>perl -wMstrict -le "my $seq = 'xxxTATAATGyyyTatAtAtzzz'; my $box = qr{ (?i) TATA [TA] [TA] [TAG] }xms; ;; my @TATAs; while ($seq =~ m{ ($box) }xmsg) { push @TATAs, [ $1, $-[1], ]; } ;; print qq{matched '$_->[0]' at pos $_->[1]} for @TATAs; " matched 'TATAATG' at pos 3 matched 'TatAtAt' at pos 13` [download] Updates: Note: The character class definition `[T\|A]` in the OP is probably not what you want. The `\|` (pipe) character has no special meaning in a character class; it just represents a literal `\|` character, so the character class `[T\|A]` matches a single one of any of three characters: 'T', 'A' or '\|'. Changed example code to use case-insensitive matching per OPed example. Note that in matching long strings, case-insensitive matching may impose a significant performance penalty; it may be better to convert all strings to a common case, then match without case sensitivity.	[reply] [d/l] [select]
Re: positions of multiple matches by mrstlee (Beadle) on Nov 05, 2011 at 19:11 UTC
Here's how to match and set the pos in one line: `use re 'eval'; my $seq = 'xxxTATAATGyyyTatAtAtzzz'; my $box = qr{ (?i) TATA [TA] [TA] [TAG] }xms; ;; my @TATAs; my @matches = $seq =~ m{ ($box) (?{ push @TATAs,[$+,pos() - length $+] }) }msxg; print "matched '$_->[0]' at pos $_->[1]\n" for @TATAs;` [download] The 'magic' is in the (?{ ... }) construct. This allows you to insert perl into your regexen.	[reply] [d/l]
Re: positions of multiple matches by Anonymous Monk on Nov 05, 2011 at 15:42 UTC
thanks a lot!	[reply]