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Match and Extract String with Regex

by monkfan (Curate)
on Nov 17, 2007 at 01:39 UTC ( #651361=perlquestion: print w/ replies, xml ) Need Help??
monkfan has asked for the wisdom of the Perl Monks concerning the following question:

Dear fellow monks,
I have these two strings:
my $str1 = 'AT1G71260'; my $str2 = 'AT1G71260_|_chr1';
How can I extract element of $str2 that match with $str1, such that in the end the extraction just give this as results:
my $results = 'AT1G71260';
Note that these two strings can contain any characters (even whitespace, semicolon(;), etc) and of any lengths.

Regards,
Edward

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Re: Match and Extract String with Regex
by ikegami (Pope) on Nov 17, 2007 at 01:47 UTC

    Are you asking to find the Longest Common Subsequence (LCS) of the strings? Searching for that should reveal nodes on the topic.

    Or if all you want to do is check if $str1 is in $str2, then index will do the trick.

    if (index($str2, $str1) >= 0) { ... }
      Searching for (Longest Common Subsequence) should reveal nodes on the topic.
      ... only if they understand how/why Longest Common Subsequence is a generalisation of Longest Common Substring.

      While it's an interesting area in which to educate oneself, String::LCSS does exactly what you need.

      -David

        String::LCSS does exactly what you need.

        I don't want to bash String::LCSS, but the implementation seems to be the naive O(n^3) algorithm instead of the O(mn) dynamic programming solution (http://en.wikipedia.org/wiki/Longest_common_substring_problem). A quick and dirty (and not thoroughly tested) implementation is much faster (although probably buggy).

        sub lcss2 { my ($s, $t) = @_; my $z = 0; my $m = length $s; my $n = length $t; my @S = (undef, split(//, $s)); my @T = (undef, split(//, $t)); my @L; my @ret; for my $i ( 1 .. $m ) { for my $j ( 1 .. $n ) { if ($S[$i] eq $T[$j]) { $L[$i-1][$j-1] ||= 0; $L[$i][$j] = $L[$i-1][$j-1] + 1; if ($L[$i][$j] > $z) { $z = $L[$i][$j]; @ret = (); } if ($L[$i][$j] == $z) { push @ret,substr($s, ($i-$z), $z); } } } } # warn Dumper \@L; return join '*', @ret; }
        my $s1 = '6'x 200 . 'zyzxx'; my $s2 = '5'x 200 . 'abczyzefg'; my $count = 1; timethese($count, { 'String::LCSS' => sub { String::LCSS::lcss( $s1, $s2 ) }, 'dynprog' => sub { lcss2( $s1, $s2 )}, });
        Update: Took the opportunity to learn XS and wrote String::LCSS_XS.
Re: Match and Extract String with Regex
by mwah (Hermit) on Nov 17, 2007 at 09:00 UTC

    If it's only that simple kind of problem that you mentioned (find one string in another string), then Ikegami's solution (index) should suffice. If you need to do that by regex, try:

    ... my $str1 = 'AT1G7. +126[0]*'; my $str2 = 'AT1G7. +126[0]*_|_chr1'; ... (my $results) = $str2 =~ /\Q$str1/g; print $results if $results; ...

    Regards

    mwa

Re: Match and Extract String with Regex
by lima1 (Curate) on Nov 17, 2007 at 10:13 UTC
    If you just want to extract the TAIR id, you could use this regex:
    my ($tair_id) = $str2 =~ /(AT\dG\d{5})/i;
    If you want to fetch the alternative splice form suffixes as well (e.g. AT1G71260.1), you could use:
    my ($tair_id) = $str2 =~ /(AT\dG\d{5}(?:\.\d+)?)/i;

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