Re: Regex /g and interpolated lengths

Well, that would depend entirely on your data, wouldn't it? Your regex looks for the desired string (e.g. "ctaac"), followed by exactly $len other characters. When I run that it works perfectly:

$allseq="ctaacjkjfggctaatlkj";
$len=3;

while($allseq =~ /(ct(?:a|g)a(?:c|t))(?:.{$len})/g)
 {push(@array, $1);}

print join("-",@array)."\n";
[download]

prints

ctaac-ctaat
[download]

What were you expecting? Do you maybe want {0,$len}? arbitrary characters?

Debugging is twice as hard as writing the code in the first place. Therefore, if you write the code as cleverly as possible, you are, by definition, not smart enough to debug it. -- Brian W. Kernighan

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Re^2: Regex /g and interpolated lengths by Anonymous Monk on Nov 15, 2005 at 21:57 UTC
Sorry I thought it would be easier to answer and didn't want to burden you with code. But here comes now the important part of the code.. I hope there is all you need and I did't forget anything. open(FILE, "<", $multiz); my @content = <FILE>; close FILE; s/^\w\w\t(.+)(?:\n)?/$1/ for(@content); my $len = length($content[0]) - 5; my $allseq = join("", @content); my @branchPoints; while($allseq =~ /(ct(?:a\|g)a(?:c\|t))(?:.{$len})(ct(?:a\|g)a(?: +c\|t))(?:.{$len})(ct(?:a\|g)a(?:c\|t))(?:.{$len})(ct(?:a\|g)a(?:c\|t))(?:. +{$len})(ct(?:a\|g)a(?:c\|t))(?:.{$len})(ct(?:a\|g)a(?:c\|t))(.*)/ig) { my $dist = length($7); push(@branchPoints, "\nBranchpoint:\t$1\t$dist\n\t\t$2\t$d +ist\n\t\t$3\t$dist\n\t\t$4\t$dist\n\t\t$5\t$dist\n\t\t$6\t$dist\n\n") +; } print REPORT @branchPoints; [download] File $multiz comes here: `aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac` [download] 20051115 Janitored by Corion: Fixed formatting, code tags	[reply] [d/l] [select]
Re^3: Regex /g and interpolated lengths by tirwhan (Abbot) on Nov 15, 2005 at 22:07 UTC
Hmm, your formatting seems a little messed up there, especially the file data doesn't look like what your code seems to be expecting. Could you please repost that, with `<code></code>` tags around the code and data? Debugging is twice as hard as writing the code in the first place. Therefore, if you write the code as cleverly as possible, you are, by definition, not smart enough to debug it. -- Brian W. Kernighan	[reply] [d/l]
Re^4: Regex /g and interpolated lengths by Anonymous Monk on Nov 15, 2005 at 22:10 UTC
Sorry I thought it would be easier to answer and didn't want to burden you with code. But here comes now the important part of the code.. I hope there is all you need and I did't forget anything. open(FILE, "<", $multiz); my @content = <FILE>; close FILE; s/^\w\w\t(.+)(?:\n)?/$1/ for(@content); my $len = length($content[0]) - 5; my $allseq = join("", @content); my @branchPoints; while($allseq =~ /(ct(?:a\|g)a(?:c\|t))(?:.{$len})(ct(?:a\|g)a(?:c\|t))(?: +.{$len})(ct(?:a\|g)a(?:c\|t))(?:.{$len})(ct(?:a\|g)a(?:c\|t))(?:.{$len})( +ct(?:a\|g)a(?:c\|t))(?:.{$len})(ct(?:a\|g)a(?:c\|t))(.*)/ig) { my $dist = length($7); push(@branchPoints, "\nBranchpoint:\t$1\t$dist\n\t\t$2\t$dist\n\t\t$3\ +t$dist\n\t\t$4\t$dist\n\t\t$5\t$dist\n\t\t$6\t$dist\n\n"); } print REPORT @branchPoints; [download] File $multiz comes here: `aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac` [download] 20051115 Janitored by Corion: Fixed code tags	[reply] [d/l] [select]
Re^5: Regex /g and interpolated lengths by duff (Parson) on Nov 15, 2005 at 22:18 UTC
Re^6: Regex /g and interpolated lengths by KaiAllard (Initiate) on Nov 15, 2005 at 22:21 UTC
Some notes below your chosen depth have not been shown here
Re^5: Regex /g and interpolated lengths by tirwhan (Abbot) on Nov 15, 2005 at 22:14 UTC
Re^5: Regex /g and interpolated lengths by tirwhan (Abbot) on Nov 15, 2005 at 22:32 UTC
Re^6: Regex /g and interpolated lengths by KaiAllard (Initiate) on Nov 15, 2005 at 22:37 UTC
Some notes below your chosen depth have not been shown here
Re^2: Regex /g and interpolated lengths by Anonymous Monk on Nov 15, 2005 at 22:03 UTC
Sorry beeing confusing. All lines should be joind so I want to find all "aligned" words that match the regex part (ct(?:a\|g)a(?:c\|t))(?:.{$len}) and this six times as there are 6 sequeces. Your code does function but it is not what I want. Thank you anyway.	[reply]