Dear all,

I'm searching a whole list of sequences of letters for a specific pattern. My problem is that the pattern isn't very specific by nature: 


$hydphb='GAFIVL';
$polar='DEHAW';
$charged='DGYAH';

$_ =~ /[$polar.$charged]([$hydphb]|[$polar]|
     H[$hydphb][$polar][$hydphb]W){18-24}[$polar.$charged]/;

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So basically, Im looking for a sequence bound by [$polar.$charged] with 18-24 letters in it, only 4 of the letters can be $polar, and this motif must be there too:

H[$hydphb][$polar][$hydphb]W.

The letters in the motif are included in the total number of letters, and the $polar in the motif must be included in the 4 $polar limit.

I was thinking about doing it in two passes: 

$_ =~ /[$polar.$charged]
       ([$hydphb]|[$polar]){18-24}
      [$polar.$charged]/;
$_ =~ /H[$hydphb][$polar][$hydphb]W/;

[download]
If the sequence matches both times, and I count the number of polar to be 4 then I can return true.

What do you think?

Cheers
Sam

In reply to Searching for character classes of various quantities AND a motif by seaver

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