Re^4: Regex /g and interpolated lengths

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

Comment on Re^4: Regex /g and interpolated lengths Select or Download Code

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Re^5: Regex /g and interpolated lengths by duff (Parson) on Nov 15, 2005 at 22:18 UTC
Off hand I'd say that you aren't accounting for the newlines in the data. You're trying to match across all six lines explicitly, but aren't matching the newlines. Try changing where you set `content` to look like this: `chomp(my @content = <FILE>);` [download] And then there shouldn't be any newlines in `$allseq` Oh, and if you're trying to match the same pattern several times, you can do something like this: `/pattern{6}/` Though in your case that'll throw a kink into how you get the values out with `$1` and friends. duff	[reply] [d/l] [select]
Re^6: Regex /g and interpolated lengths by KaiAllard (Initiate) on Nov 15, 2005 at 22:21 UTC
`s/^\w\w\t(.+)(?:\n)?/$1/ for(@content);` [download] Newlines should have been removed by that line.	[reply] [d/l]
Re^7: Regex /g and interpolated lengths by duff (Parson) on Nov 15, 2005 at 22:29 UTC
Ah, good point. Perhaps the file was generated on a DOS/Windows based system but he'se running his program on a unix-based or Macintosh system? The newlines would be different between those systems and his RE wouldn't be working properly. duff	[reply]
Re^5: Regex /g and interpolated lengths by tirwhan (Abbot) on Nov 15, 2005 at 22:14 UTC
Almost :-). It's `<code></code>`, not `<code><\code>` 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] [select]
Re^5: Regex /g and interpolated lengths by tirwhan (Abbot) on Nov 15, 2005 at 22:32 UTC
Running that code gives `Branchpoint: ctgac 34 ctgac 34 ctgac 34 ctgac 34 ctgac 34 ctgac 34` [download] What were you expecting? If this is not the output you are getting, then I'd guess duff probably has the answer 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^6: Regex /g and interpolated lengths by KaiAllard (Initiate) on Nov 15, 2005 at 22:37 UTC
No sorry the machine is a Windonws system so no confusing \r or whatever. Yes what I want to get is all aligned Branchpoints. So it should be: `ctgac 34 ctgat 18 ctaac 0 ctgac 34 ctgat 18 ctaac 0 ctgac 34 ctgat 18 ctaac 0 ctgac 34 ctgat 18 ctaac 0 ctgac 34 ctgat 18 ctaac 0 ctgac 34 ctgat 18 ctaac 0` [download] or something like that despite of the format. But it should find all Branchpoints ... not the first one and then surrender.	[reply] [d/l]
Re^7: Regex /g and interpolated lengths by KaiAllard (Initiate) on Nov 15, 2005 at 22:43 UTC
My thinking was that it reaches the end of the string so it breaks up with only one found brachpoint. May it be the solution?	[reply]
Re^7: Regex /g and interpolated lengths by tirwhan (Abbot) on Nov 15, 2005 at 22:56 UTC
Your code measures the length of the line only once and then matches the given pattern and any characters up to the end of the line, after which it starts at the beginning of the next line. This should do what you want: `while(my $line=<FILE>) { my $linecopy=$line; while ($line=~m/(ct[ag]a[ct])/g) { my $match=$1; my ($rest)=$linecopy=~m/(?:$match)(.)$/; print "$match\t".length($rest)."\t"; } print "\n"; }` [download] Update:* Or, if you're into recursion: `sub matchit { my $data=shift; if ($data =~ m/(ct[ag]a[ct])(.)$/) { print "$1\t".length($2)."\t"; matchit($2); } else { print "\n"; } } matchit($_) while(<FILE>);` [download] 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] [select]